Just making sure. I know that you know better, but in the case of that one person, the only patch he applied didn't affect core Rockbox at all. It was JUST a plugin, with no API changes or anything, yet when he used a clean build downloaded from the Rockbox site it didn't show the problem. His rockbox.ipod should've, technically, been a 'clean' one but for some strange reason it was behaving oddly.
Okay, next question: Have you verified in the debug menu that dircache is actually active? Sometimes even if you've turned it on, and it's scanned at boot, something will go wrong.