PCI-E slot possibly not working (P67A-GD53)

Hello all,
New guy here. New MSI customer and everything.
I just built a new PC today with a MSI P67A-GD53. I first plugged in the VGA (a MSI GeForce GTX 560Ti OC Twin FrozR II) to the top PCI-E slot.
On boot, I get what I think is a VGA problem beep code (1 long - 3 short beeps). This happened with 2 different VGAs. I also tried my old XFX 8800 GT.
The computer boots fine when I plug in the MSI VGA to the second (bottom) PCI-E slot.
Does this mean that the top slot is broken? I guess I could try the 8800 at the same time to see if it works when 2 VGAs are plugged in, but I suspect it wont. Should I get the motherboard replaced? I am considering not getting it replaced now since I ordered it from the UK and I live in Cyprus and replacement could take a month to complete (posting overseas). Would that be a bad idea? I fear that if one part of the motherboard is faulty, it could potentially have other problems as well.

Full hardware list
New stuff:
Intel Core i5-2500K 3.30GHz (Sandybridge) Socket LGA1155 Processor
MSI P67A-GD53 Intel P67 (Socket 1155) DDR3 Motherboard ** B3 REVISION **
Corsair Vengeance 8GB (2x4GB) DDR3 PC3-12800C9 1600MHz Dual Channel Kit (CMZ8GX3M2A1600C9)
MSI GeForce GTX 560Ti OC Twin FrozR II 1024MB GDDR5 PCI-Express Graphics Card
Samsung SpinPoint F3 1TB SATA-II 32MB Cache
(pardon the verbosity: I just copy pasted the order I made recently).
Old stuff (from previous setup):
Corsair TX850W PSU
Quote from: Wonkanoby on 17-August-11, 20:29:22
are you sure you got the stand offs right under the board
I might have missed a hole, but I definitely didn't leave any old stand-offs that might short the board from underneath.
I'll recheck and add any missing and get back to you.

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