PPCFreak: Hard reset two front soft keys + the reset button. Will confirm with a screen asking if you want to clear it. You should have also seen this when you installed the rom or you may have other issues still on your device! YOU MUST HARD RESET.
When you hard reset, it will clear all reg values, apps, shortcuts, etc from the device (not storage card) and will go back to the rom default values and locations. Thus moving the exe back to the windows dir (and startup) at this point should be using all default (unmodified) values. When you installed the app it reset all reg values, mapping, etc so you are using a different config now than the defaults.
-saridnour