I am using the 1024 firmware, the only change on top of that is adding the new frequencies into cgminer.lua. All six units stable again at the lower frequencies with no voltage setting.
Trying again on one unit, this time with ckolivas's S3 cgminer 4.6.1 build, also deleting --queue and adding --lowmem. I can't think of anything else to try. The S3's are in a ventilated space, so the ambient temperature over the three hour period is constant. Why would I get great results for 1+ hours, but poor results over 3 hours?
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Possibly easier to simply post a shot of your web UI, but I'll ask just in case:
1. What temps do you have on that rig?
2. What is the HW %
3. What freq are you running at?
4. If you've recently started the rig, could you post the cgminer startup string (usually logged in system log ...?)?
5. Finally, could you also post the freq setting line that you are running from the cgminer.lua file?