physx is bugged for the game. After trying the fix listed in this (gog) forum for the game I would get massive slowdowns any time a special effect (blue or green spheres from background obelisks) was on-screen or I approached the area that had one.

I disabled physx outright (I did it through the DefaultEngine.ini though it might work with just XEngine.ini) and noticed that it also fixed the auto-save stutter in the process where it'd freeze for a second any time an auto save occurrred.

Search for:

[Engine.Engine]
bDisablePhysXHardwareSupport=False

And change it to:

[Engine.Engine]
bDisablePhysXHardwareSupport=True