Oh, that's a shame. I used a Gigabyte Radeon X800XL, and the heatpipes actually intrude slightly into the recess on the VGA duct, so it fits like a glove as long as the fan's inside the duct and not mounted in the external recess. I understand that the heatpipe cooler on this card is made by Zalman but that it's a little different from their retail versions. I guess that's the case or else the PCIe-16X slot is in a different place on your mobo. I was hoping my situation would apply in your case.
