I just realized this during the move from a nearly unsupported OpenSUSE-system to a Debian 6.0. During the restore of my virtualmin backups, only one virtual server is shown for restore.
It seems as if this is due to the fact, that the .info-file only shows data for the last backed up virtual server, not all.
From where and how are you trying to restore? Are you using SSH, local files or something else? In what format was the backup taken (one file per domain etc.)?