After I removed the Accelero X2 cooler that comes with my video card and replaced with a Zalman water block with Nautilus 500 water cooler, my video card no longer is able to run any games for more than 3 minutes. I don´t think its overheating because the temp is much lower with the water cooler.
It definitely sounds like you have thermal issues as your video card is mostly idling while doing basic Windows tasks. I don't think you "destroyed" your video card... you've just caused it not to function properly. It is odd that you said your GPU is not overheating, but I suppose there are other components that could be overheating as a result of your change. Perhaps the fan on that card circulated air over some other components? Sure, the GPU is staying nice and cool, but you might have killed the airflow over some other components (memory comes to mind)
If you are able to see your screen with no problems not under load the card is fine. It should be a cooling issue. I had a problem with my ATI X850XT video card when I removed the stock cooler and installed a water block. When I rebooted all I could see was multicolored lines and could not see the screen at all to access BIOS menus. I sent mine back to ATI and within 2 weeks had a replacement that works fine til this day in my media center system.
I would disassemble your waterblock setup on the card and check all components on the card to make sure nothing was bent or broken and reapply a moderate amount of thermal paste and retry.
As others stated here I would try adding some type of fan that can blow directly on the card to aid in cooling the memory modules and other components that may have been cooled with the stock cooler.
If none of this works then you should remove the waterblock and reinstall the stock cooler and contact ATI for your RMA number and you will get a repair or replacement part in approx. 2 weeks.
I would not go into the fact that you removed the stock cooler, they never asked me and I never volunteered that info and I doubt they even looked at my card close enough to see it.
Be sure if you have to mail your video card to ATI that you put your RMA number on the outside of the box and you package the card with at least 2 inches of clearance on all sides of the card. Only send the card and nothing else because they will not send any items other than the card back to you.
Are you cooling the VRM in someway?
If not, I'll bet thats the issue.
Install Everest and turn on logging. Run your games - then check the GPU VRM temps. If your near or over
120C then your to hot.
The later Accelero X2's come with a heat spreader for the VRM - if you don't have that you can purchase one through Arctic. On my x1950 pro, I actually added some ram sinks onto of the spreader to increase surface area, and then tacked on a small fan for extra cooling. In the worst case now I never get over about 88C on the VR chips.