Jetguy has pointed out a very important issue that can come up for people using MakerWare 2.2.0 with their Thing-O-Matic's: if you enable custom profiles, the resulting gcode will cause your heater to be turned on at the end of the print *without* regulation.
Read more: https://groups.google.com/d/topic/jetty-firmware/MhkQKSpDo0s/discussion