Games are not loading its own config files

[TerrorizedGakon]

Like in the title, I can't get any game to load its config file, it keeps loading the default one instead. I don't know why, as it used to work correctly. Exe file names are correct. I have windows 7 64 bit.
Uninstalling through removing everything in safe mode, including the registry files with appinit and then reinstalling did not help. I went back to an older version 2136 and that also did not help. What can be the cause?

EDIT: Actually, CoD 4 seems to be loading its config file, but most things seem to get overriden by the default config... I have no clue.