Filemon output shows that in case 1 and 3, the App Paths is used to locate examdiff.exe. In case 2, X2 tries to open examdiff in folders in the path environment setting but not in the App Paths folder.
x2 doesn't read this particular key
to save you a complex explanation, the easiest solution is to add your examdiff path to your PATH environmental variable. Then it will work