Чтобы в лог писались сообщения "Connection from 10.5.0.112 rejected" DebugLevel должен быть 5 или выше. А у вас он 0: "Debug level set to 0". Уровень дебага можно выставить при запуске демона параметром -D5(уровень дебага)  или параметром в конфиге: DebugLevel=5

[15-Jun-2016 19:20:38.647] Log file opened
[15-Jun-2016 19:20:38.648] [INFO ] Additional configs was loaded from /etc/nxagentd.conf.d
[15-Jun-2016 19:20:38.648] [INFO ] Debug level set to 5
[15-Jun-2016 19:20:38.648] [DEBUG] Data directory: /var/lib/netxms
[15-Jun-2016 19:20:38.648] [DEBUG] Subagent API initialized
[15-Jun-2016 19:20:38.650] [DEBUG] Validating ciphers
[15-Jun-2016 19:20:38.650] [DEBUG]    AES-256 enabled
[15-Jun-2016 19:20:38.650] [DEBUG]    Blowfish-256 enabled
[15-Jun-2016 19:20:38.650] [DEBUG]    IDEA disabled (config)
[15-Jun-2016 19:20:38.650] [DEBUG]    3DES enabled
[15-Jun-2016 19:20:38.650] [DEBUG]    AES-128 enabled
[15-Jun-2016 19:20:38.650] [DEBUG]    Blowfish-128 enabled
[15-Jun-2016 19:20:38.650] [DEBUG] Crypto library initialized
[15-Jun-2016 19:20:38.657] [DEBUG] SQLite version 3.8.7.1
[15-Jun-2016 19:20:38.657] [INFO ] DB Library: Database driver "sqlite.ddr" loaded and initialized successfully
[15-Jun-2016 19:20:38.657] [DEBUG] New DB connection opened: handle=0x9e12a0
[15-Jun-2016 19:20:38.795] [DEBUG] Local database opened successfully
[15-Jun-2016 19:20:39.805] [DEBUG] Linux: using /sys/block to distinguish devices from partitions
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda1 isRealDevice=0)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda2 isRealDevice=0)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda3 isRealDevice=0)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda4 isRealDevice=0)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda5 isRealDevice=0)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sda6 isRealDevice=0)
[15-Jun-2016 19:20:39.806] [DEBUG] Unable to parse /proc/drbd, DRBD data collector will not start
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=sr0 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd0 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd1 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd2 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd3 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd4 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd5 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd6 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd7 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd8 isRealDevice=1)
[15-Jun-2016 19:20:39.806] [DEBUG] ParseIoStat(): new device added (name=nbd9 isRealDevice=1)
[15-Jun-2016 19:20:39.807] [DEBUG] ParseIoStat(): new device added (name=nbd10 isRealDevice=1)
[15-Jun-2016 19:20:39.807] [DEBUG] ParseIoStat(): new device added (name=nbd11 isRealDevice=1)
[15-Jun-2016 19:20:39.807] [DEBUG] ParseIoStat(): new device added (name=nbd12 isRealDevice=1)
[15-Jun-2016 19:20:39.807] [DEBUG] ParseIoStat(): new device added (name=nbd13 isRealDevice=1)
[15-Jun-2016 19:20:39.807] [DEBUG] ParseIoStat(): new device added (name=nbd14 isRealDevice=1)
[15-Jun-2016 19:20:39.807] [DEBUG] ParseIoStat(): new device added (name=nbd15 isRealDevice=1)
[15-Jun-2016 19:20:39.812] [INFO ] Subagent "linux.nsm" loaded successfully
[15-Jun-2016 19:20:40.814] [DEBUG] External parameters providers poller thread will not start
[15-Jun-2016 19:20:40.815] [DEBUG] Data sender thread started
[15-Jun-2016 19:20:40.815] [DEBUG] Data collection scheduler thread started
[15-Jun-2016 19:20:40.815] [DEBUG] Database writer thread started
[15-Jun-2016 19:20:40.816] [DEBUG] Data reconciliation thread started
[15-Jun-2016 19:20:40.816] [DEBUG] Thread pool DATACOLL initialized (min=1, max=64)
[15-Jun-2016 19:20:40.816] [DEBUG] Session agent connector disabled
[15-Jun-2016 19:20:40.816] [DEBUG] Trying to bind on 0.0.0.0:4700
[15-Jun-2016 19:20:40.816] [DEBUG] Trying to bind on [::]:4700
[15-Jun-2016 19:20:40.816] [INFO ] Listening on socket 0.0.0.0:4700
[15-Jun-2016 19:20:40.816] [INFO ] Listening on socket [::]:4700
[15-Jun-2016 19:20:41.818] [INFO ] NetXMS Agent started

Всё... 

Похоже, я что-то упустил, а теперь нервы и напряжение при поисках упущенного не дает мне это разглядеть. Всё должно быть проще... Типа, надо серверу сказать, где находится агент, но как... 

Проверять следующее:

• Сервер не может подключиться к агенту(данные о фозможностях агента сервер получает во время Configuration poll)

Проверить:

• Агент запущен
• У агента в конфиге прописан IP сервера
• Проверить лог агента на строчки вроде: "Connection from 10.5.0.112 rejected"
• Проверить Firewall

cat /var/log/netxmsd 
[14-Jun-2016 18:53:56.647] Log file opened
[14-Jun-2016 18:53:56.683] [INFO ] Platform subagent "/usr/lib/x86_64-linux-gnu/netxms/linux.nsm" successfully loaded
[14-Jun-2016 18:53:56.707] [INFO ] Database driver "sqlite.ddr" loaded and initialized successfully
[14-Jun-2016 18:53:57.116] [INFO ] Network device driver "DLINK" loaded successfully
[14-Jun-2016 18:53:57.125] [INFO ] Network device driver "DELL-PWC" loaded successfully
[14-Jun-2016 18:53:57.126] [INFO ] Network device driver "H3C" loaded successfully
[14-Jun-2016 18:53:57.126] [INFO ] Network device driver "AIRESPACE" loaded successfully
[14-Jun-2016 18:53:57.127] [INFO ] Network device driver "PING3" loaded successfully
[14-Jun-2016 18:53:57.128] [INFO ] Network device driver "NETSCREEN" loaded successfully
[14-Jun-2016 18:53:57.133] [INFO ] Network device driver "ERS8000" loaded successfully
[14-Jun-2016 18:53:57.133] [INFO ] Network device driver "PROCURVE" loaded successfully
[14-Jun-2016 18:53:57.134] [INFO ] Network device driver "QTECH-OLT" loaded successfully
[14-Jun-2016 18:53:57.135] [INFO ] Network device driver "CATALYST-GENERIC" loaded successfully
[14-Jun-2016 18:53:57.136] [INFO ] Network device driver "NTWS" loaded successfully
[14-Jun-2016 18:53:57.136] [INFO ] Network device driver "HPSW" loaded successfully
[14-Jun-2016 18:53:57.137] [INFO ] Network device driver "CATALYST-2900XL" loaded successfully
[14-Jun-2016 18:53:57.137] [INFO ] Network device driver "MIKROTIK" loaded successfully
[14-Jun-2016 18:53:57.138] [INFO ] Network device driver "TB" loaded successfully
[14-Jun-2016 18:53:57.139] [INFO ] Network device driver "CISCO-ESW" loaded successfully
[14-Jun-2016 18:53:57.139] [INFO ] Network device driver "CISCO-SB" loaded successfully
[14-Jun-2016 18:53:57.140] [INFO ] Network device driver "UBNT" loaded successfully
[14-Jun-2016 18:53:57.140] [INFO ] Network device driver "AT" loaded successfully
[14-Jun-2016 18:53:57.141] [INFO ] Network device driver "BAYSTACK" loaded successfully
[14-Jun-2016 18:53:57.141] [INFO ] Network device driver "SYMBOL-WS" loaded successfully
[14-Jun-2016 18:53:57.456] [INFO ] Listening for SNMP traps on UDP socket 0.0.0.0:162
[14-Jun-2016 18:53:57.456] [INFO ] Listening for SNMP traps on UDP socket [::]:162
[14-Jun-2016 18:53:57.457] [INFO ] Listening for client connections on TCP socket 0.0.0.0:4701
[14-Jun-2016 18:53:57.457] [INFO ] Listening for client connections on TCP socket [::]:4701
[14-Jun-2016 18:53:57.457] [INFO ] NetXMS Server started
[14-Jun-2016 18:53:57.457] [INFO ] Listening for mobile device connections on TCP socket [::]:4747
[14-Jun-2016 18:53:57.457] [INFO ] Listening for mobile device connections on TCP socket 0.0.0.0:4747

cat /var/log/nxagentd 
[14-Jun-2016 18:56:41.983] Log file opened
[14-Jun-2016 18:56:41.983] [INFO ] Additional configs was loaded from /etc/nxagentd.conf.d
[14-Jun-2016 18:56:41.983] [INFO ] Debug level set to 0
[14-Jun-2016 18:56:41.992] [INFO ] DB Library: Database driver "sqlite.ddr" loaded and initialized successfully
[14-Jun-2016 18:56:43.166] [INFO ] Subagent "linux.nsm" loaded successfully
[14-Jun-2016 18:56:44.168] [INFO ] Listening on socket 0.0.0.0:4700
[14-Jun-2016 18:56:44.168] [INFO ] Listening on socket [::]:4700
[14-Jun-2016 18:56:45.170] [INFO ] NetXMS Agent started

root@deb2:/var/log# netstat -tupln|grep xms
tcp        0      0 127.0.0.1:21784        0.0.0.0:*              LISTEN      8397/netxmsd   
tcp        0      0 0.0.0.0:4701            0.0.0.0:*              LISTEN      8397/netxmsd   
tcp        0      0 0.0.0.0:4747            0.0.0.0:*              LISTEN      8397/netxmsd   
tcp6      0      0 :::4701                :::*                    LISTEN      8397/netxmsd   
tcp6      0      0 :::4747                :::*                    LISTEN      8397/netxmsd   
udp        0      0 0.0.0.0:162            0.0.0.0:*                          8397/netxmsd   
udp6      0      0 :::162                  :::*                                8397/netxmsd   
root@deb2:/var/log# netstat -tupln|grep agent
tcp        0      0 0.0.0.0:4700            0.0.0.0:*              LISTEN      8742/nxagentd 
tcp6      0      0 :::4700                :::*                    LISTEN      8742/nxagentd 

/etc/nxagentd.conf 
# Log File
LogFile=/var/log/nxagentd

# IP white list, can contain multiple records separated by comma.
# CIDR notation supported for subnets.
#MasterServers=127.0.0.0/8 # и так пробовал
MasterServers=127.0.0.1

 iptables -L
Chain INPUT (policy ACCEPT)
target    prot opt source              destination       

Chain FORWARD (policy ACCEPT)
target    prot opt source              destination       

Chain OUTPUT (policy ACCEPT)
target    prot opt source              destination   
   
iptables -L -t nat
Chain PREROUTING (policy ACCEPT)
target    prot opt source              destination       

Chain INPUT (policy ACCEPT)
target    prot opt source              destination       

Chain OUTPUT (policy ACCEPT)
target    prot opt source              destination       

Chain POSTROUTING (policy ACCEPT)
target    prot opt source              destination     

Сервер и агент на одной машине. И кажется мне, что сервер к агенту даже не пытается достучаться.
 Такое впечатление, что я не указал серверу, где искать агентов.

• Сервер не может подключиться к агенту(данные о фозможностях агента сервер получает во время Configuration poll)

Проверить:

• Агент запущен
• У агента в конфиге прописан IP сервера
• Проверить лог агента на строчки вроде: "Connection from 10.5.0.112 rejected"
• Проверить Firewall