Credit also to Nezroy for pointing me in the right direction. He is correct that this is caused by the cgminer not recieving instructions for freq settings and he saved me a lot of time trawling through code.
His solution would work in theory but I believe there is a better beginner friendly way.
With the most recent firmware installed, go to the tabs, System ==> Miner configuration ==> Advanced settings. And re-select the default freq for your device. then hit "save and apply". No power reset required. This will load the missing values back in.
For those that care, I believe this is caused by the "keep settings" box being ticked on the firmware update. This causes problems for those of us that are updating from the original installed cgminer by bitmain, to the updated cgminer v4.6.1 at firmware S320141013. The OS is probably trying to import the old freq settings into the new cgminer in an incorrect format. Those that don't tick this box on firmware update probably wont have this problem as default values will be used. Those that update between versions S320141013 and S320150109 firmware also are probably not affected as cgminer versions are unchanged.
Hope this helps.
By the way, your S3 is still profitable??
I bought two of them and run them where I live. The power is included with my rent, so my only condition is that they need to run near where I sleep. The S3 is the only one that I think I can get away with the custom fans making them near silent, (Nanoxia deep silent 120mm fans). That is the reason I still run them. I would love more powerful units as power cost is not an issue, but the extra heat needs venting and thus noisy fans. I'm very glad I've had success as a hobbyist miner, which is good, not just for me but there must be others in the community that can say that taking the gamble paid off and spread the word.
The details if you're interested, I bought two of them from ebay in December 2015. One for £105 as single unit. The other for £128 with corsair cs550m inc. I then spent £96 on a corsair rm750x to power them both. So spent £329. My slush pool page says my all time payout is 0.57777511BTC which right now is £548.38 so I'm up on my investment as I hodl. And I of course still have the hardware to sell if my circumstances change.
tl:dr yes it's profitable, free power, but slow returns due to low power units, but silent as in close proximity to where I sleep.
I've got a few running in my home simply because other miners are too loud or unreliable. There's really no alternative for me since I need the quiet in my house :/