Problems with DVD or Graphics card

I have just built a new system. I am running win xp pro on an asus sli premium mobo w/athlon 64 x2, asus 7800 gtx, plextor 716sa (latest firmware), I have more than enough power and ram. Initially I used a pata drive to load operating system and drivers because I was aware of some compatability issues between plextor drives and motherboards. After installing the OS and mobo drivers, I configured my wd raptor on serial port 1, maxtor on serial port 2, and the plextor on serial port 3. Since I used the non raid serial ports, I assume Im running in nonraid configuration. The first problem I encountered was installing a flight sim game. It appeared to install ok but when the game started it was shaking slightly and a couple of reinstalls failed to fix this. Then it was a little strange because I managed to install a couple of games that installed and play perfectly. Then I installed a game that locked my pc up on the opening install screen and I had to reboot to unlock it. I did that 3 times with the same result from that specific game. Next I installed doom 3 and it seemed to install ok but when I clicked on the desktop icon to open the game, nothing happened. I did hear either my hard drive or the optical drive spooling up as though it was going to start the program but nada? I called the asus tech support and he suggested that I uninstall my graphics card drivers and get the latest drivers from Nvidias website, which I did with no apparent effect. One thing I noticed was when I open up Ntune (graphics utility), it posts a warning that says my pci clock is tracked to the HT bus and that if I change the HT clock that it will also change the PCI clock and damage my system. I don't know if that has anything to do with my problem but I could not find anything in the mobo manual about setting the pci clock. Help!