The Extreme is pretty much the top dog and will stay that way for some time. The guys put heaps and heaps of R&D into that board, in fact I recall saying in October at the media launch in London to a TV chappie that the motherboard is a game changer and I still think that. From a sheer performance perspective it is tops.
And what you have to remember is that the PCIe management is on the CPU these days not really on the motherboard, what the motherboard design does is maximise that potential and without doubt ASUS have done this with the Extreme. Oh and I am not a blind fanboi either. When SB came out the UD7 board was king for 3D benching the first 6 months, and I still have 4 of them.
To help us help you - please provide as much information about your system and the problem as possible.