(Assuming you are having the issue of the miner dropping to 10% (ie. 50GH/s) hashing output after a bit.)

This issues description matches exactly the problem I experienced with the first December firmware I experienced after upgrading..

Why are they shipping new controllers when you could just reflash with the firmware that didnt have this issue..

I had the same problem.. I downgraded fixed the problem straight away..

https://www.bitmaintech.com/support.htm?pid=007201407180243004432lBQW28O0633


From Web Interface: System Tab, Backup / Flash Firmware Tab, Hit "Choose File" under Flash New Firmware Image section, Upload the latest BIN file from the link above.  

Problem solved!  (I assume it was a bad cgminer binary, nothing to get anyones panties in a bunch about.. the S3/S3+ is a very nice miner.)