Well I gave Coinotron a try today and the same issue. So it doesn't seem to be a pool issue. No pretty graph on their pool to show you but:

GUIMiner (litecoin edit)
Default settings for Radeon 7950 = Steady 296kh = Pool speed ~300kh
Change Intensity to 16 = Steady 484kh = Pool speed ~100kh

Tested over at least 100 accepted shares on both Stratum and not. Same result.
So it seems for some reason the increased hashing speed locally is resulting in lower hashing speed on the pool.

I read another guy saw a similar issue: http://forum.litecoin.net/index.php/topic,1957.0.html

I think it does matter what hash speed is reported on your pool's end as that's the result of valid shares and rewards dished out.

Still unresolved.