I am still very much puzzled i have tried many different pools tried everything that is based in EU only and i still get bad reports on Khahs. Could it be internet signal? At moment i am having 3 of 5 in quallity of wireless. I really dont know what else could be.
did you try both cards separately? maybe one just can't handle the config. also try upping the voltage a little bit on the one card and see if the perf goes up (stability reasons).
oh, and are you talking about pool kh/s or what is displayed on the terminal? if you making anywhere near what similar miners are making, I would just ignore it(click the "pool" button on the pool website and look for similar kh/s).
edit: ping test the pools and post what numbers you get.