I've just set up my miner, Radeon 290x on CGminer with a .bat exe.
CGminer gives me approx 700kh/s but the pool only records around 20kh/s (I've used both coinotron and multipool and they are same).
How long did you have your miner running before checking the pool stats? I'm not sure if a 24/hr average is an accurate period, but in my experience letting it run for a good 10-15 minutes before checking your pool stats is a good way to get more accurate information.
I actually seem to suffer from the opposite problem - my work PC does scrypt CPU mining 24/7 and generates about 92kh/s according to minderd.exe - but my pool always always registers as higher. As high as 125kh/s at some points.
Anyone have any idea why this is happening? I'm not interested in changing it, but I would like to understand it.