Hi,
there was an issue in an older Release of XI 3.1. If the Win AD connectivity got lost, all Groups where deleted in the CMC. Could be that this was the issue within XI 3.1 SP3 as stated by JRK. If you are on a newer Release then you should be fine.
Basically everything has been told here.
Maybe this Best Practice for 3rd Party Groups can help you:
http://service.sap.com/sap/support/notes/1895948
http://service.sap.com/sap/support/notes/1857539
Regards
-Seb.