I recently upgraded from a EVGA GTX 460 SE to a MSI GTX 660 Twin Frozer and reviews and benchmarks that i've seen from this card looked very good to me but when I installd the card it semed to work fine until I booted up Saints Row the Third and got 30fps on all settings. I also did a Passmark benchmark and the average score for the 660 is 3953 and I got a 2677. I tried updating my drivers to the latest ones and that didn't improve anything.
My PC Specs are
MB: Asrock 760gm-gs3
PSU: A 600 or 650 Watt i'm not sure
CPU: AMD Phenom II X4 965 BE
RAM: 2 Sticks of G.SKILL Value Series 4GB 240-Pin DDR3 SDRAM DDR3 1333
HDD: Samsung by Seagate Spinpoint F3 HD502HJ/ST500DM005 500GB 7200 RPM 16MB Cache SATA 3.0Gb/s 3.5" Internal Hard Drive -Bare Drive
I also had a similar problem with my 460 SE but it was not nearly as severe.
I was thinking it might be the Motherboard since it is rather cheap and maybe it has a low bus speed for the GPU i'm told but I want to be sure of the problem before I go replacing things.