Added two bug entries about this:

Single File Scanner progress bar corrupt
Single File Scanner group mixing

The SP2 thing was a good hint; it might have to do with how Windows passes opened files; in this case, each file that is selected opens one instance of SDFiles which then communicates with the first one, telling it which file to scan. This is synchronized, but should probably be so for each set of files, not for each file entry.

I tested with drag'n'drop of a bunch of files first, where the problem does not appear (drag'n'drop sends a list instead of each file separately).