Yes, we have seen this too. I *think* what is happening is that the userids are not 'fixed up' properly. The userids relating to who you are having a conversation with do, of course, need to be changed to reflect the ids on the new (target) Moodle. This doesn't seem to be getting done so they get corrupted. I'll try and have a look and post a sensible bug report later on.
Bug #2194 was filed about backup/restore. I found and hopefully fixed bugs in both the backup and restore routines. The fixes are in CVS (development version).