Here's an updated S3 binary.
http://ck.kolivas.org/apps/cgminer/antminer/s3/4.6.1-141020/cgminerRecommended if you're mining on p2pool for the default binary actually discards stale shares which you should never do, especially on p2pool. Also includes changes to queuing and memory usage that were necessary on S4 but probably only of minor benefit here. Recommend you edit the cgminer startup script to remove the --queue value entirely, and add --lowmem. Performance should be pretty much unchanged.