I'm not completely sure why my profits were lower on MPH, but I have some suggestions.
Firstly, it seems that MPH systematically overestimates ZEN value compared to whattomine. So, MPH will choose to mine ZEN more often than it "should".
Secondly, there is an extra fee for auto-exchange, that I use. It's only 0.2%, but it's not zero.
Thirdly, as for all switch-mining, in the time it takes to mine, confirm, transfer and exchange, the price of the coin may have fallen.
Lastly, the switch algorithm itself may be a culprit. MPH seems to continuously check which coin is the most profitable, but it won't switch until it finds a block of whatever it is mining at the moment. I think this is done to offset the penalty imposed due to the PPLNS payout scheme. But it has a serious backside. If a coin that MPH mines suddenly gets a big difficulty spike, it won't switch until a block is found, no matter what. I've seen my own miners churning away on a high difficulty ZEC for a couple of hours even when ZEC was at the bottom of the whattomine list.
My theory is that the autoswitch pool is so big on MPH it actually "moves the market". As soon as MPH identifies a currency for the autoswitchers to move to, about 10MH+ switch to the new currency and spike difficulty just from their move alone. So the currency from which the autoswitchers moved sees a difficulty drop and those mining that currency still get the benefit.
Just a theory, but I found autoswitch wasn't as good as dedicating to one currency which was consistently overperforming on WTM over the last 24-48hrs.