I can say that I had same issue when I tried wafflepool for a day.  The same settings that were stable on middlecoin (although pushed to the limit) were causing lockups on wafflepool.  Wafflepool switched difficulties far more often, maybe this has something to do with it.  I had to go back to almost stock clocks to mine there.

BTW: my not-so-empirical test showed waffle was about 70% less profitable.  My theory is that their hashrate is still small, so when the switch to a coin, they have low chance of finding a block.  This is compounded by spending only a few minutes on each coin, leading to lower payouts.  If this makes sense, then we all should thank mimiminer and sfire.