In the nightly build 999.201612310331 the snmpd spits out a lot of warnings on the config file.

Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 9: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 10: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 11: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 12: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 13: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 14: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 15: Warning: Unknown token: smuxpeer.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 16: Warning: Unknown token: smuxsocket.
Jan 2 13:16:53 ROUTER snmpd[5943]: notificationEvent OID: linkUp
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 23: Error: unknown notification OID
Jan 2 13:16:53 ROUTER snmpd[5943]: notificationEvent OID: linkDown
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 24: Error: unknown notification OID
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 25: Warning: Unknown token: monitor.
Jan 2 13:16:53 ROUTER snmpd[5943]: /etc/snmp/snmpd.conf: line 26: Warning: Unknown token: monitor.
Jan 2 13:16:53 ROUTER snmpd[5943]: net-snmp: 2 error(s) in config file(s)

After some comparison with VyOS 1.1.7 hosts i found that part of the issue is the changed startup options.
This can be found in /etc/default/snmpd

VyOS 1.1.7:
SNMPDOPTS='-LSid -Lf /dev/null -u snmp -g snmp -p /var/run/snmpd.pid'

Vyos 999.201612310331:
SNMPDOPTS='-Lsd -Lf /dev/null -u snmp -g snmp -I -smux,mteTrigger,mteTriggerConf -p /run/snmpd.pid'

Although this change was probably on purpose, when i change it back the messages do not appear and BGPD connects again with the SNMP daemon.