I have noticed several times (that is it does not happens all the time, but occurs regulary) that VSS has forgoten my working folder settings and re-set it to be a root of the C: drive.
It is very annoying to find out that some of the files you have checked out and been working on are not in the same folder where you expect them to be (and it also pollutes the drive with a C:\SubProject1, C:\SubProject2 folders instead of keeping them all inside of C:\Work).
Any recomendation to prevent VSS from doing this again and again. And yes, please, don't recomment switching to SVN, CVS, TFS etc - there are the rules I can't change.