Great project!! Just finished building mine for a school project (research lab wouldn't loan me the FLIR camera). Max I noticed you removed the pull-up resistor note on your website - don't know if this was on purpose, but I connected the sensor directly to A4 & A5 and it's working without a problem.
I used the EEPROM update, it too worked without any problems. The surface temperatures I am getting seem accurate. This sketch is also a good way to be sure that you have the sensor connected properly - If it doesn't read the inital values, check your connections. Just unplug the 'duino before uploading the new values if you don't want them.
In reference to dvernor's question, I was having some trouble with the Java software too. I could get it to calibrate but when I started the scan, the program would hang. Uninstalling 64-bit Java and using 32-bit fixed it; working great now.
Other troubleshooting item - when I started the Java program for the first time, to calibrate, the arrow buttons didn't respond - I found that it was just out of range, if you press a button in the same direction for long enough the servos eventually respond...
Thank you for sharing all of your hard work on this!