Hoping this answers your question better than above:
A few months back before getting more mining gear I was running two Spartan x6500s (
http://fpgamining.com/products/x6500-rev2)
I had them running on mpbm. (before using a stratum proxy, perhaps it may work differently now...I'll try it and let you know what I find)
I found that when attempting to run BTC pool AND alt pools at the same time on the hardware, that while they seemed to all mine and play nice at first, eventually, one of the blockchains will take over and hog your hashrate. I had been running bitminter as well as a terracoin pool and a freicoin pool all within the same instance of mpbm. Within a day, Freicoin had taken over my entire hashrate despite terracoin and bitcoin pools running. So then I figured it was related to the pool and decided to switch over to something else like just terracoin and bitcoin. Within a day, surprise surprise, terracoin had taken over my hashpower altogether. That is when I figured out that you should only mine one blockchain per instance of miner software running. Now that I have more hashpower in the form of a 60 block erupter array, I am mining the be's on BFGminer (mining gigahash.io via my
Cex.io account so that I can easily convert earnings to hashpower on the spot) while still instituting mpbm on the fpgas with them mining joulecoin.
