Hi Magnus
This is weird. The exclusion filter is about page and hibernation files, some drivers could also be removed during reconfiguration, but data files sould not be skipped!
I suppose you should have shrinked some volume which has triggered file level cloning. Block level cloning (which is default) copies clusters and doesn't understand files. This could be a possible workaround.
Another possibility is that these files got into the source machine after conversion has begun.
Can you attach the task's log files to have a look?
Regards
Plamen
