Indeed, I've seen region mods do this exact sort of thing, especially if there is a poor connection on one of the data lines. As a matter of fact, I missed any mention earlier in the thread that this system had a region mod on it.
The region mod would've been my #1 suggestion to check had I realized you were working with a system that had a region mod.
Still, the best thing you could do at this point is try the cart in a different, non region-modded system and see what happens. You might be surprised at the results.