So I posted in MOG, Makerware version 2.1 was the first to support T-O-M. It assumed and still does in 2.2, that you have a MK7 or MK6 using 1.75mm filament.
The only way to edit the profile is to make a new one from template. Doing so in Makerware 2.1 resulted in the start and end .gcodes being wrong for the T-O-M since they defaulted to a Replicator 2 profile. The new problem is that 2.2 fixed the start.gcode but still uses the wrong end.gcode on the custom profile (and that's the only way to adjust for filament diameter that I can see) and it issues an M127 command. In another thread, it's documented the M127 command can cause the HBP to heat up uncontrolled at the end of a print.
So, this is a note of extreme caution to T-O-M users seeking to use Makerware, watch your bot at the end of a print. Monitor the HBP heater. DO NOT PRINT unattended.
Most of those go without saying but in light of this new bug, they have even more importance than normal.