I notice with Multipool when it mines a fast block time coin stales increase and reported MH/s drops significantly below what's reported by CGMiner. When it switches to a longer block time coin like LTC/NVC reported block time is correct. Middlecoin probably suffers from something like this. Stales are supposed to be priced in so even though it reports less it should still be making more money.
In fact I don't price in stale shares into the profitability yet. Only orphans.
That is next on my list, now that I understand it.