Make sure the project is in the VSS and is checked out before you save it.
Make sure you are checking in the right VBP file.
When you compile, before checking in, does the revision number change in the Project Properties?
EDIT 1 (October 29, 2012):
Please follow the steps below and tell me the result:
- Check out the project (including VBP file, make sure you get the latest version from SourceSafe)
Open VBP, the Auto Increment option is checked and Version Number section has valid numbers (Major/Minor/Revision)
Work on the project, compile EXE, check if Version Number section has new Revision number
Check in all files (including VBP) into SourceSafe
Close project
Get latest VBP file from the SourceSafe, open it, check version number numbers