Often, the reason is that EM is trying to enumerate too many databases (see
KB #282416). There is a threshold in Enterprise Manager, beyond which it just can't handle enumerating the entire list of databases and keep their references in memory. So, if you really need to challenge the limit of 32,767 databases on a single server, don't expect Enterprise Manager to be a very effective management tool.
Make sure your databases are not set to "Auto-close"... right-click each database, choose properties, and go to the options tab.
Make sure ODBC tracing is disabled on both the client and the server. You can configure this option in the ODBC applet in the control panel.
Have a look at
KB #889696 to see if an updated system procedure will relieve the symptom.
Finally, make sure both the source and target servers are at the latest service pack. See
Article #2151 for information on keeping your server up to date.