There's something about the integration between Microsoft's SourceSafe product and VisualBasic that causes SourceSafe to get very confused about directories:
It reverts to using the Windows "8.3" mangled file names for directories and quickly becomes very confused about what directory it should be in and what directories files are checked out to.
Be careful: As you create, remove or rename directories, it may switch to an incorrect directory on you and really mess things up.
Check files in from the wrong directory.
Be unable to check in files, as it can't find the directory. (...with no error message; it just silently doesn't do the checkin.)
I make it a habit to edit my "ss.ini" file on a regular basis and delete out all the working directories except the root.
It still gets confused sometimes, but this at least minimizes the pain.
Very irritating that when setting a working directory it puts everything in upper case, effectively screwing Java PackageNames?.