This is always a pain, no matter what source control system I have used (Visual SourceSafe, CVS, ClearCase, etc.). The binary .frx files always cause a problem when merging Visual Basic forms.
I know...I know...why are you using Visual Basic...because there are lots of legacy applications still written using it and although I hate to admit it, I actually like using it (ducks tomatoes).
You need to just bite the bullet and include them in version control system. Unfortunately, they do contain information that isn't available anywhere else in the source. (The bitmaps added to ImageList controls, for example.) If you lose those files, you can't rebuild the application correctly.