Stratix V FPGA kit card only running at Gen3 pre-set 7

I'm no PCIe expert, by my understanding after I read the spec is that a gen 3 endpoint is required to operate at the highest speed supported by the root complex. I does not imply that this is selectable. Assuming your device is a card that plugs into a PC, for full compliance testing you would need to verify it with 3 different motherboards, one that supports gen 1, one at gen 2 and one at gen 3 speeds. Conversely, if your device is a motherboard/root complex, you would need to test it with gen 1, 2, and 3 cards.