I have investigated this problem with Mouttie through teamviewer and it turned out that the updater do not replace files the way it supposed to.Thanks for your work but I sill have the same problems. I have version 3.2.0.3 and the Game Tweaker crashes when I enable the "Disable H.Acceleration" or the "Normal mouse" checkbox in the performance profiles. It causes an NullReferenceException.
How to fix this?
Go to AOE2Tools installation folder and you should find a zip file "newupdate.zip" > Open it and extract "Gamer Tweaker.exe" to replace the other one that exists there in the same folder.
I'm currently investigating why the updater do not update files on some winwodws machines.