The GOG version is the Ubisoft version, not the original. There are a few differences, most importantly the game engine. All of the fan-made fixes were based on the original game. Some (IIRC) will work equally well on both versions. The TELP patches will not.
It sounds like your game is failing to switch video control back to lithtech.exe. One of the steps in that process isn't working. Presuming that you have changed the compatibility and permission settings of 'lithtech.exe' as well as 'mm9.exe', I'd suggest that you un-install and re-install from your copy of the original, fix permissions and compatibility, apply your crack, fix the DLL, and see if the game runs. If it does, then apply the TELP 1.3a patch. If not, then the problem is either with the graphics drivers or the registry.