Geforce gtx 560 ti not running in pci express 2 0

Hello,
I just purchased an Nvidia GTX 560 Ti and it is only running at PCI-E 1.1 in a 2.0 slot, my old ATI Radeon HD 5750 that it replaced ran at 2.0 in the same slot. I can't figure out why this is, any suggestions?
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More about geforce running express
  1. How do you know that it is running at PCI-E 1.1?
  2. I downloaded the latest GPU-Z program, I think I may have figured out what the problem is. It clocks down to save power when not running a program so it might clock it's PIC-E setting as well.
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