Just upgraded video card....need help

Hello,First of all here are my specs:Intel Pentium 3.2 dual core2GB DDR2 RAMWindows XP w SP2 FS9.1OLD video card was GeForce 6800NEW video card is GeForce 8800 GTS with 620 MB VRam(btw, I went from 20-25 FPS with medium to medium high settings in dense areas to 40 fps with ALL sliders MAXED out.... incredible increase in performance. 8800 is a fantastic card).BUT............Since I installed the new card I have noticed a few "bugs" with payware aircraft that were definitely not there before. For example, I loaded the PMDG 747-400 on the runway at SFO and loaded a KSFO-EDDF stored route. Once I took off the auto pilot would not engage; it kept giving the loud a/p disconnect warning sound every time I tried to engage it (I was attempting to engage it after the gear was up and the doors were closed). One of those times I pressed it it suddenly engaged. Then once it crossed the RBL way point the route disappeared and the airplane began to turn left to right to left to right. I realize this is the PMDG forum but I also had a payware 767 and when I took off on a normal takeoff the aural warning kept saying "Terrain! Terrain!" even though I was nowhere near any terrain.So does anybody know if after you install a new video card you should reinstall FS9 and all the addons? Or is there something else going on here? Any help is greatly appreciated. Thanks,Darren