Weird problem that has me baffled.

You should have a look at the apache logfiles. There you will find the real path to the file that was not found. This could give you a hint if it is different then what you might expect.

On a ubuntu server I once looked for a few hours before I found out why some javascript files where not loading. On Ununtu some package (common-js) is installed on a default lamp stack. That package placed a global alias for /javascript/ for every virtual host. Man what was I pissed when I finaly found the reason why my own javascript files where not found...

Perhaps you are running into something similar!