I don't know if anyone else has noticed, but it seems like alot of the problems to do with games working from the hdd are random... What works for one, doesn't for another...
My guess is, this is due to something simple... So I ask you folks having problems, your directory structure...
Are you burying the games in 15 sub-dirs?
Are you naming the folders for the games with spaces?
Are you making the folder names unnecesserily long?
Are you renaming default.xbe?
Take the game that has been fucking up on you the most, put it in the root of f with a folder name 8 chars or less, see if that fixes it..
The reason I say this is because this is how I've setup my xbox (albeit f is a god damned mess), and i've yet to try a game that didn't work flawlessly off the hdd... I mean, I have 60 games on it so I haven't tried every one in depth, but every one I have tried has seemed to work just fine.