I have the same combo and it works very good over here.
Next to what Jim said I would also create a manual library backup after importing those files, then you don't have to import again and again, simply restore the library until the issue is fixed.
After MC12 is done importing, check this folder:
C:\Users\YourUserName\AppData\Roaming\J River\Media Center 12\Library
I asume you have installed Vista on C:. Also, replace "YourUserName" with your real user name of course.
I think it should contain something like 60 items and be about 4MB in size (give or take 1MB)?
Keep the folder open and close MC, watch those files and start MC again and see if it changes.