I think I've been able to locate the error now!
And it actually isn't an Apache problem at all, but it's related to rewrites and the vBulletin integration of Photopost..
I had a few relative URLs to images in my vBulletin navbar and headinclude templates, and when it tried to locate the image files it did of course use the rewritten directory as the path.
And since it first tries to locate the directory before the actual image file then the "file does not exist" error didn't report the image file since it stops to look when it doesn't find the directory first..
I've replaced all of the relative image URLs in the templates with absolute URLs now and most of the errors are gone from the log, but not all so it may be other URLs that are generating these errors as well.
I'll do some more testing and post here if I find out more...