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So the motherboard may shut off the PCI express lanes if it see's something plugged into the PCI x1 lane? Anyone else have this issue. I want to know before I invest some cash into some cables.

No, just with the x16 lanes. It's meant to move the speeds around depending on how many cards you have plugged in, as I can tell. It's one of the MSI 890 (? might be wrong on the number..) with 5 x16 slots, and can handle 4x16 cards. It is also spaced to allow 3 cards plugged in with a space inbetween the three of them. If memory serves, with three cards in they are all actually working at x8, and it disables the one x16 slot that isn't covered with a gfx card. With 4 cards plugged in they all run at x4, and it turns the last one off but its covered by a dual slot gfx card anyway. In the manual it has a fancy table with which slots get which speeds depending on whats plugged in. I wish you could force it in bios, then I'd just force all the slots to x1 =]
Not sure why, but with any card plugged into any of the x16 slots, I could not get it to see a card with a x16->x1 extender in the single x1 slot that the mobo does have. With no other cards installed the one on the x1 extender would work. Wierd. Got her stable with three cards in it, I need to get some more extenders to experiment more.

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