Okay surprise surprise.. with two cards if I toggle HBC on card #1 it works just fine. If I toggle HBC on #2 (previously working) now card #2 disappears from Crimson.. it's always the "last" listed card in Crimson. This is quite interesting.
Dude, have you flashed your bios to the latest version?
Otherwise try another mobo.
Or play around with the PCI-E settings in bios. It sounds like there could be some inconsistencies there.