This message shouldn't really warrant WARN level logging and would would be more interesting as INFO:
2011-12-06 18:23:16,288 WARN [LinkdScheduler-3 Pool-fiber2] HibernateEventWriter: processIpNetToMediaTable: Setting OnmsAtInterface MAC address to 00220d805441 but it used to be '' (IP Address = 172.31.255.3, ifIndex = 100)
and this one:
2011-12-06 19:14:38,879 WARN [LinkdScheduler-3 Pool-fiber1] HibernateEventWriter: processIpNetToMediaTable: Setting OnmsAtInterface ifIndex to 3 but it used to be '-1' (IP Address = 172.31.255.2, MAC = 001ae3719541)
likewise for this:
2011-12-06 19:14:39,727 WARN [LinkdScheduler-3 Pool-fiber0] HibernateEventWriter: processRouteTable: No node ID found for next hop IP address 192.168.1.1. Not adding the IP route interface to the linkable SNMP node.
These aren't inherently something wrong, but just musings on what makes linkd tick over.