Stratum disconnect is normal when coins change. Make sure you don't run anything newer than cgminer 3.5.0 as they added a 5 minute delay for fail-over that could lead to you mining your backup or maybe nothing for up to 5 minutes even though hash cows only dropped out for 10-20 seconds to switch coins.
Thanks, but i'm using 2.11.4 and still getting extended disconnects. I check the stats page, and we're still mining the same coin.