Ok now this is a nasty bug.
I moved a domain that had several aliases and when you choose which domains to move I saw a check box for all those aliases as well so I checked them.... That wasn't a good idea :(
Creating backup of cuffstuff.ch on www.openstream.net ..
.. created backup of 20.26 MB.
Downloading backup of cuffstuff.ch in file cuffstuff.ch.tar.bz2 ..
.. download of 20.26 MB complete.
Uploading backup of cuffstuff.ch in file cuffstuff.ch.tar.bz2 to mcqueen.openstream.ch ..
.. upload of 20.26 MB complete.
Deleting cuffstuff.ch on www.openstream.net ..
.. deletion complete.
Restoring backup of cuffstuff.ch on mcqueen.openstream.ch ..
.. restore of cuffstuff.ch complete. Domain move was successfull!
Creating backup of cufflinks.ch on www.openstream.net ..
.. backup failed : Virtual server cufflinks.ch does not exist
Creating backup of cuffstuff.biz on www.openstream.net ..
.. backup failed : Virtual server cuffstuff.biz does not exist
Creating backup of cuffstuff.info on www.openstream.net ..
.. backup failed : Virtual server cuffstuff.info does not exist
Creating backup of cuffstuff.net on www.openstream.net ..
.. backup failed : Virtual server cuffstuff.net does not exist
Creating backup of cuffstuff.org on www.openstream.net ..
.. backup failed : Virtual server cuffstuff.org does not exist
Refreshing status of 2 systems ..
.. done
You see why ?
So for the domain screen you should NOT have any check marks for any alias or sub-servers/domains.