Every motherboard manual says to insert a single GPU into slot one for best performance. In my case, the ASUS X99-E WS has seven identical PCIe 3.0 x16 slots. Why, then, does it still recommend putting it into slot 1 only? My problem is that the CPU cooler and fans are too large and overhangs the slot. Physically impossible to go into slot 1. I have had it in slot 3, but I'm wondering if it is costing me some performance.
I know that I can find a smaller heatsink, but that's not the point. I'd like to know what makes slot 1 different than the others for a one-GPU configuration? According to the IRQ assignment chart, all of the slots are shared in column A, except for slots 2 and 3 are shared in column B. (I have no idea what that means, btw)
The main reason I ask is that this computer has never performed well. Rendering and file export is slow, even for the GeForce GTX 780. And the USB3 ports on this system are slow and some don't even detect when a drive is plugged in. ASUS wants me to ship the motherboard back RMA, but these were my observations in troubleshooting.