Disclaimer: I have little to none understanding of how pools work.
From my understanding, each share holds a certain "weight" depending on what difficulty you are mining on.  So if say you are mining at 256 difficulty then each share has 1/2 the value as if it was at difficulty 512.  So just speculating, it is possible that the shares that are valid and the shares that are stale have different weights since the pool uses vardiff and your difficulty may have changed somewhere.

Feel free for someone to correct me or validate my understanding.
**edit** Looks like I was mostly wrong 


I do have another suggestion for the pool.  It seems that the worker stats are reset every minute which leads to a huge variance.  One minute it reports 20MH/s for me and the next 8MH/s.  It would be very nice if it could be averaged out over a longer period of time such as 15 minutes or so.