There's a few technical differences between a PCI-e 2.0 and PCI-e 2.1 card, but a PCI-e 2.1 card is not "faster" than a PCI-e 2.0 card. Which PCI-e 2.1 card so you have?
Basically the difference between PCI-e 1.x and PCI-e 2.x is the bandwidth. The newer standard has twice the bandwidth of the older standard. Unless you have a really, really powerful card, the PCI-e 1.x slot should have enough bandwidth.
I have a Radeon HD 5850 PCI-e 2.0 card in a PCI-e 1.0 slot and it runs fine.