Let me know if this is unsupported, but I think I found a bug (or my misunderstanding of the capabilities) in cgminer.  I'm running cgminer on BAMT with a GPU mining bitcoins and everything works just fine 24/7. 

I wanted to check out some FreiCoin (sha256d), so I added a second pool to my list of pools in cgminer.conf and then set rotate to 5 minutes.  My expectation is that every five minutes I would alternate between mining BitCoins and FreiCoins.  Everything seemed to work the first day, but the second day the BitCoin pool had some connection problems (stratum connection interrupted) and it kept switching between the pools.  Unfortunately it seemed that it would submit BitCoin work to the FreiCoin pool and vice-versa.  I got quite a few strange errors, including 'H not zero' replies from the pools.  Sorry, I don't have a good log right now.

Is this supposed to work?  Is there a better way to achieve this goal of mining two types of coins on the same hardware?

-E

P.S.  Thanks for the great software.