Even with the new cgminer file, my units are doing a little worse than with the previous one. I am guessing I am losing around 10-14 GH/s per device, which is not bad but when you have 11 of them it makes a slight difference.
Do you have the latest firmware on them? i had exactly the same experience with my batch 6 units and reverted to the stock cgminer, however (again as is documented in this thread), when I updated to the latest firmware, which I had to do when upgrading my S1's, I get the same result as the stock, or slightly better, but with the security flaws plugged.
Yeah I have the latest firmware, it is dated 8/26/2014. My issue is probably the 5 batch 1 miners I have, even though some of my batch 5 units are a little slow as well.