I had this for a long time - i guessed it's not a "core" (code) issue as no one else has reported it as a "bug".
I had this on my cpanel servers running trunk (3.0) for a while, but i seem to have fixed it - so now you're gonna want to know how, right...?
And now i can't remember how! I tried all the .htaccess files, the perms on the files themselves, but no joy - but in the end i sort of decided it was a local set-up issue so didn't document my fix!
I really can't work it out now, but if you're still stuck i'll have another go tomorrow - i did manage it, just can't work out how now...