If you want to disable the onboard 3D video card, you really should disable it in the BIOS, not just Windows Hardware Profiles.
First, you'll want to enter your BIOS. This is done differently depending on what type of computer you have (usually, you have to press delete or one of the "F" keys at the top of the keyboard once your computer starts up). To find out what applies for you, look at the bottom of the screen when your computer first starts up. It should say "Type xxx to enter setup". This is the key you want to hit.
Now, depending on your BIOS, the location of your onboard video card settings might differ. Once you find this, make sure that instead of listing an IRQ number, it says "Disabled". This will (hopefully) once and for all disable the onboard video.
It's possible that your problem is not related to the onboard video at all. In this case, more information would be required to troubleshoot your problem.
Good luck.