I'm not sure what could have gone wrong there. I imported several flac files over the weekend there and their [file type] field is correctly filled.
Do they play?
You could select one file, then edit the file type field, entering the following: =right([filename (name)],4) and pressing enter.
If that works for you, you could select all of the others at once and repeat the above and MC will process them all in swift order.
That should fix things, but does not help much with resolving why things needed fixing in the first place, and I'm a bit bemused with that. Maybe someone else will have some thoughts...
-marko