Wierd problem with games 2D and videos going way too fast after one hour or so.

So, I'm having this wierd problem with many games.
After an hour, many games seem to forget to look at FPS limits, and just go as fast as possible.
For an example, Star Wars Knights of the Old Republic
When there is 3D, nothing seems out of place, but when I go to the pause menu, the blinking images just go super fast.
And if there is a video clip, it lasts like half a second, when it zooms trough it +350FPS.

It's a wierd bug, but what is even more wierd, is that if I put my computer to Stand-by mode, for like 2 seconds, and then start it back, every game works good for an another hour.
After that, the blinking reoccurs, and I have to put the comp in Stand-By again.

And it looks like it does not care if I'm playing something.
When I start my computer at morning, when I come back from school and try to play something, the blinking is there.

Anyone have any clues what is wrong and how I can fix this ?

List of games that have problems:
Star Wars Knights of the Old Republic, Menus, and all screens that have only 2D start going +350FPS and blinking super fast. Also, some text's just scroll by in a second, and it is impossible to read them.
GTA San Andreas, All cutscenes (even when they are full 3D scripted events) are skipped, showing like 1second from the start.
Flatout 2, Start videos zoom trough in 1 second, all menus blink like hell.

Machine spec
ASUS A8N-SLI premium
AMD Athlon 64 X2 4200+
Radeon x1300PRO
2048mb Kingston RAM
Win XP Pro

I have tried Reinstalling windows and changing drivers from Ati to Omega and back.
I have no idea what is wrong...
Please, someone help ._.

 

I had this problem with GTA San Adreas, problem was solved by setting the affinity to just one core. If I'm right the games will be trying to use bother cores thinking its one, hence running twice as fast.

Set the affinity by right clicking the program in processes of task manager and set the affinity to just one core. If this works then you can set the affinity permanently by adding "-A1" or "-A0" to set the core (sans quotes).

 

well willywonka's solution has worked for me!

 

I noticed the problem in Flatout 2 on mine until I downloaded the AMDX2 cpu driver. 2nd from bottom

 

Thank you \o/
Installed that, and I have been playing KOTOR for 3 and half hours straight after almost 8h Idling, and it hasn't bugged even once
I need to check GTA and Flatout some other time, its 3:12AM here, gtg sleep.
Thank you :3
You really saved me