Yo man,
I set my cards like this:
x1 --- empty
x1 --- Xonar D2X
x16 --- HD 5970
x8 --- empty because my video card cooler blocks the slot
x16 --- empty (very same reason like x8)
PCI --- empty
x8 --- Palit GTS 250
I had never any problems so far. The GTS 250 was detected by the very first time:up
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