I don't have the build environment to create a full binary image, and the code will need a LOT of work to actually become part of mainline cgminer it seems, but for the time being here is a link to a bugfixed binary of cgminer 4.6.0 for the S3 based on the bitmain code. Copy the file into /usr/bin/ on the S3 overwriting the existing one:
http://ck.kolivas.org/apps/cgminer/antminer/s3/4.6.0-140908/cgminer
http://ck.kolivas.org/apps/cgminer/antminer/s3/4.6.0-140908/cgminer
Wow if this works as I'm sure it will I think we owe ckolivas a BIG thank you.
Will give it a shot. Expect a tip to your BTC address ckolivas !
Strato