QUOTE
i deleted my cache in e: and the saves folder for the games that don't work
This could just be semantics and that I'm misunderstanding you, but I normally go into Micro$oft Dash and then find and delete the prior save file for the entire application in question (in this case FCEUltra and/or MednafenX). Or, I just navigate to the TDATA and UDATA folders via FTP and trash the saves in question.
Then, using my Chris Farley Ninja Skillz , I completely delete the offending folder of the misbehaving application/emulator - be it in your E, F, or G partition. Then, when no one is looking, I rub my rosary and do a completely "clean" install. This way there's neither a save file, .ini file, nor offending remnants of the prior emulator left behind to piss you off.
Granted, with emulators, I always leave the rom folders behind so I don't have to re-up them (too time-consuming).
You may have meant this, but perhaps not. It certainly won't hurt to try.
Let me know, mang.