Ah. That would explain that.
In regards to the directories: I would look around the web for stuff in regards to that, but I know that mod_include (SSI) isn't very configurable. I haven't had much experience with it, but I doubt there is anything I could do from my end to change that behavior.
If I were you, I would try to contact some Apache folks (maybe go on Apache's IRC channel) and ask them if this is the expected behavior and why. If there's something I should change on my end I'd be glad to help you out.
Sorry I couldn't help more