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I noticed it was down on the website. It said the last share was submitted 4 days ago by worker 3. I will leave it a few days and try reinstalling the update. Is there anything i can show you or give to you if it happens again to diagnose the fault? If so i'm happy to help.
Well at this point I can only suggest running it without the update - since I'd expect it to have the same problem.
Note that unless you can reproduce the problem over a specific time range, you may find that switching between versions will have the expected random effect of "who knows when the problem will happen again"
One thing to look at with my cgminer version would be the stats output - e.g. temperature and usb errors.
The usb errors in the S3 aren't true usb errors, but rather show problems talking to the fpga that runs the chips.
If you have another computer you could periodically (every 5 minutes?) run and log an API summary+devs+estats and look for a pattern in that leading up to when it happens.
I did get someone with hundreds of S3s to test it and they are still using it, so I would have expected some response if it was failing after a period of time, thus I'd expect it to not be a cgminer issue.