Mobo chipset and GPU compatility?

This might sound stupid but guess this is where to find out.

Do graphics cards and like company chipsets, (ie NV mobo chipset and a NV card or ATI chipset and GPU vise versa), more stable when paired with each other or does it not matter?

The reason I'm asking is my motherboard is a Asus A8N5X socket 939 with a Nvidia chipset, I had a 6800 GS and when playing certain games I had no problem at any save/objective points ect. I replaced it with a x1950xtx, I did make sure I completely removed the old driver so as not to cause any issues.

Now the same save/objective spots in certain games nothing happens, the programed scene doesn't take place. For example blowing up a flak cannon, the AI that was supposed to do it just sit there looking around doing nothing even though all objectives leading up to that are completed. If I go back to the nvidia card problems solved, weird huh?

Any possiblility to a NV chipset and ATI card not being 100% compatible or could there be something else the problem here?