Are you running the November S3 firmware version? I experienced a similar issue running the November firmware, but after switching to the 10-24 firmware my S3s have been rock solid.
The November firmware release contains a bug that causes S3s to slow down significantly after hashing for a few hours. It looks like Bitmain has removed the November S3 firmware from their website due to this issue.
Agreed, anything but the beta firmware I posted past 1024 should be avoided. 1024 also breaks the reset button, my beta one fixes it.