[GrenSo]

Do you delete before the reinstallation all files and profile files of SH3?

Which OS do you use and do you try compatibility mode for the .exe files?

You can also try with MultiSH3 on current or on new user a second SH3 profile.
Another idea is, to create as test a new user on the OS and test SH3 with this new one.

And yes, it is a really strange issue... Maybe you can try, if possible, to install it on another PC. I'm sure, that this issue came from your PC and not from the game.