Ok, I apologize. I thought you were referring to the hash rate estimation we display on our website.

Yes, you are correct, your miner will always display your "true" hash rate. And that shouldn't vary between pools unless your miner is idling a lot. I'm not sure about all the various mining software, but I know phoenix very noticeably says when it's idling.

If you are using the same flags, and you are not seeing any warnings about an empty queue or idle miner, let me know what mining app (and version if known) you are using. Also, your OS might be helpful too.

If all the settings do turn out to be the same on your end, I must say, this would be a first for me. But, I don't want to rule anything out either. 

As for the hash rate on our site. Just like Deepbit or BTC Guild, the hash rate we display is simply an estimate and doesn't play a part in your earnings. Different pools are going to use different algorithms for estimating your estimated hash rate, add in some variance, and then you have a recipe for seeing different estimates no matter which pool you view.

However, I can tell you that our pool looks at your last N share submissions and calculates your hash rate based off of that. So, if you are just starting mining with us, or if there was a gap in your mining (eg, stopped your mining software to reconfigure it, etc), then your estimated hash rate will be a lot lower. After a few shares are submitted this will level out and IMHO start to show you a pretty good estimate of your hash rate.