I don't know if you guys have noticed this or not.

Check the pins on the pcie slots.
Most of my slots only have a portion of the pins there.
Only 2 of my slots have all of it's pins.

Sure there might be specs somewhere listing this or that slot used for 16x and etc...
But it's probably best you check yourself to see what slot is capable of running full speed.

Kind of lame I think, that you can't just pick any slot and run it full speed...
But ohwell.
Better then having a bunch of 1x or 4x slots that you can't fit a full sized card in..., or maybe not ^^ ... I don't know.

Mentioning this because perhaps it may have something to do with the dual card setup probs.