Thanks Victor, I will try to put together something a bit more concrete to investigate the next time I'm on-site. 
LLDP is enabled on all switches. MNDP from Mikrotik is also enabled though which makes the neighbor list on a switch contain all the other Mikrotik switches, would this affect NetXMS? Only directly connected switches list LLDP as discovery method though.
/ tuxic
			LLDP is enabled on all switches. MNDP from Mikrotik is also enabled though which makes the neighbor list on a switch contain all the other Mikrotik switches, would this affect NetXMS? Only directly connected switches list LLDP as discovery method though.
/ tuxic