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It could be a very simple problem with an unbalanced fan blade or the blade striking something during rotation. However that should have been picked up in factory testing. Get is replaced under warranty. I can't comment on your other issue as the fan section is not anywhere near the sensor board and TEC circuit. Any of the capture software choices have configuration choice that can affect downloads, don't rush to judgement there yet. Just get it replaced and start from square one.
As a note for other ASI1600NM-C owners, i have noticed a buildup of dust on the blades of my fan and on the motor itself. This is not unusual i believe as all PC fans suffer from the same issue over time. I use my camera a lot, and it would now have over 100 running hours on it, so dust build up can be expected over time. It can be easily cleaned with a soft artist paint brush and a puffer bulb. If left it may produce out of balance vibration or reduced cooling effectiveness.
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