Electronic – Copper or Aluminum Heatsink

Maybe, maybe not, but I'd ask why you are not correlating hot chips with power supply currents, and why you're not putting a temperature sensor on the heatsink. If the thermal path from the die to the heatsink is impaired you'll get a different temperature differential between the die and the heatsink. Likewise, if the chip is drawing more current you should be able to predict the final temperature of the die based on normal thermal behavior. And measuring the heatsink temp doesn't require a dedicated contact sensor: a temporary one will do, or a non-contact IR unit should work, since the emissivity of the heat sinks should be pretty uniform.

As to why the maybes, consider the following model:

^{simulate this circuit – Schematic created using CircuitLab}

If the thermal resistance from the die to the heatsink is much larger than the thermal resistance of the heatsink to ambient, and the thermal capacity of the die is much less than the capacity of the heat sink (and I would guess both to be true), the latter is the dominant factor in determining the thermal time constant of the heatsink, and thus of the die. In this case, increases in the die/HS thermal resistance will have only small effects on the time constant of the die, but will cause the die to get hotter. You'll have to figure the values for your board to see if this is the case.

Thermo-Electric Cooler efficiency "is a function of ambient temperature, hot and cold side heat exchanger (heat sink) performance, thermal load, Peltier module (thermopile) geometry, and Peltier electrical parameters." And "A single-stage TEC will typically produce a maximum temperature difference of 70°C between its hot and cold sides. The more heat moved using a TEC, the less efficient it becomes, because the TEC needs to dissipate both the heat being moved, as well as the heat it generates itself from its own power consumption."

So a heat sink on the "hot side" alone isn't enough. The cold side gets cold quickly, having little thermal mass, and efficiency falls to a very low value. Also as the hot side warms up, each junction's internal resistance increases, drawing less current.

TECs are most efficient when both sides are the same temperature (and little heat is being moved.) The best overall working efficiency (in terms of pumping heat) may be up to about 13% of Imax. Beyond these currents, resistive heating losses increase greatly, and the device spends more power moving heat it generates itself.