I've never got round to really investigating the problem, but I had a similar on a win 2000 ADV server machine running SQL 2000.
What I found was if I closed EM and reopened it the servers reappeared one group at a time ie open EM, close EM, open EM (the first batch of servers would appear), close and reopen and the first and second batch would appear and so on.
I did also note that I had two shortcuts to EM, and one worked correctly and one didn't.
Hope this helps a little