This seems super strange. I haven’t heard of anyone else having these issues(either at our studios or on threads here) and nothing about the tool touches Maya’s systems. Only one script may have had an effect and that is the userSetup.py script, since that is a standard maya script, but again, that seems unlikely since all it is doing is adding the Epic Games menu to your menu bar on startup.
Any more information you can provide? I see you’re using Maya 2014. Is it a student license?