Are you measuring the temperature of the heatsink?
1) feedback is being accomplished with a infrared camera and calibrated blackbody that's accurate to .001*C. I set the PWM of the peltier, wait for it to level, and use the camera to match the blackbody to the peltier.
2) @DVDdoug- could you maybe explain peltiers a bit more to me? How would this having a 6A rating be causing this effect?
4) The peltier is about as flush with the heatsink as I can get it without using a press of some sort- I can fit about 3 or 4 sheets of notebook paper in between the two.
Eh? If you can fit paper in between the two, then it is not making contact at all!
Apparently, you are not using this feedback to control the PWM. Apparently, you are sending PWM values of "500" or "1000" instead of varying the PWM value depending on the feedback.BTW - What do these values of 500 & 1000 mean? The Arduino normally uses PWM values of 0-256. If you are trying to send values above 256 the last 8 bits might be getting used. In that case, the 8 least significant bits converted from a decimal number would look rather random.You are trying to "pull" 6 Amps from a 3 Amp power supply! ...What happens if you plug too many toasters & hair dryers into the wall and pull too much current? Your power supply might not have a circuit breaker like your home, but the voltage might drop, or the power supply might overheat, etc., or it might "safely" go into current limiting and cut-back the voltage.From Ohm's Law, current is Voltage/Resistance. The amperage depends on the voltage applied and the resistance of the Peltier. If the power supply cannot supply the full 6A at 12V, the voltage must drop, since Ohm's Law is a law of nature and it's always true.
Then Paul_B is right, if you have a 3-4 sheet of paper gap, they are not touching at all. Heatsink compound is to fill the *gaps* between the device and the heatsink. The best thermal transfer is when the device has 100% metal-to-metal contact to the heatsink. In the real world, this can't happen, so we use heatsink compound to fill in the gaps, so you have something better than air transferring the heat.The key is the spread the heatsink compound thinly - you should be able to see through it - and then torque it properly so that you get maximum metal-to-metal contact and the compound fills in the other gaps.