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Brendan, did I understand correctly that your hot and cold heatsinks are joined by metal? That will transfer the heat. Another thing to consider is if the cold side is getting warmed up by the fan from the hot side?
Did you use any heat transfer compound?
How big is the heat sink? If it is large, you could try running the thing at full power without the fan and KEEP AN EYE ON THE HEATSINK TEMPERATURE. Don't let it get too hot or you will kill the TEC. And don't do this without the thermal compound.
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