Joker you can delete your install of CFS3 normally yes which should be a completely separate folder from your OFF install.
Do NOT delete anything in \OBDSoftware\CFSWW1 Over Flanders Fields or \OBDSoftware\WW1Scenery.
(That's the default locations). Yes CFS3.exe is used by OFF Manager but only the one in the CFSWW1 Over Flanders Fields folder.
They should not be mixed up unless somehow you are installing INTO the same folder as CFS3 was installed?
i.e . if it is under \program files\microsoft games\combat flight simulator 3\...... or whatever then that would be bad.
To me sounds like you were lucky and got a long session with less strain on the GPU, no idea why CFS3 would change it and maybe it did not, maybe you were just lucky?
Maybe check your memory settings now, it was reset to default you say, which may not be the best or correct settings for your memory (the guys above have put a load of info re that to read through).
One thing, maybe you have different compatibility settings on cfs3.exe and CFS3.EXE and maybe they are conflicting somehow. Check them both just to see.