Not Sure about if this effects slots eg using 2 AGP or PCIe slots or if the card has 2 GPUs.

Consider the following scenario:
  • You have a Windows Vista-based computer.
  • The computer uses two or more DirectX-compatible graphics processing units (GPUs) in a linked configuration.
  • You are using a DirectX 10 application and driver.
In this scenario, the computer's graphics performance indicates that only a single GPU is being used.
CAUSE
This problem occurs because the operating system does not forward driver-render requests to the secondary GPU.

Take a look for yourself at http://support.microsoft.com/kb/936710 just choose the 32bit or 64bit fix to download. If you are running SP1 on vista I'm not sure if it was already included but you can try it and see. I dont think it has anything to do with which cards you use as it's a VIsta Bug for all people running multigraphics cards.