Edit: I read Raymond's old blog post there, and it looks like it was definitely a problem for Windows 95 so it wouldn't surprise me that it continues to be an issue.
Doesn't one of the old version checking APIs still return a version of 3.95? Or did that disappear somewhere along the way?
I think historically developers get tiered version checks wrong, because it's just too easy to get wrong. Sometimes I wonder if that's why Apple has taken to the OS X.n numbering scheme (although I suspect marketing has more to do with that one!)