From previous postings, from 6.5 to 6.5.2.a, the topology refresh seems to have been an issue. It appears NBU 6.5.4 has the same problem, unless someone can tell me how they corrected it.
I've noticed as well with 6.5 that the topology doesn't want to refresh on it's own very well nor when I just attempt to hit refresh which used to work well in 6.0. Only the Refresh All option under the view menu has been reliable at updating the topology for me. If there are solutions out there I too would be interested in hearing about them.