I'm using the multi-algo switching right now with MPH and claymores ZEC 8.0 as well as ETH/DCR 7.4 works well.

my only complaint is that the trigger for the switch is being done by a 10 minute "share not accepted" timeout function in the miner and I wish I could shorten it so that there isn't much delay in the switching. 

But it sounds like you might be trying to run both programs at the same time? thats not really how you do it maybe i Misunderstand what you are doing

your bat should just run one program at a time and cycle through the two depending on what the multialgo port says from MPH.