Well, the game version certainly does play a big role in the FPS department, but it is usually not the sole reason.
In this case, assuming these different versions are all installed at the same time, we can leave out things like graphics driver versions. Maybe some factor like a particular Direct3D version being used (Direct3D9 was the version used for the vast majority of the game’s lifespan, only expanded to include Direct3D11 & 12 after 1.36, as explained in this thread)
Can you link screenshots of the different versions and mark them? Something like the first orc tutorial mission with an FPS counter somewhere. I wanna see comparisons.