I've been trying to figure out why my TOM has suddenly developed extruder problems. It was just fine for a week or two, and then all of a sudden extrusion became a hit-or-miss affair. I was inclined to think it was a mechanical problem with the motor since I had to unseize it when I got it, and the motor would stop spinning during a time when it was supposed to be extruding even with the filament plunger backed completely out so there was no load on it. The only way to get it moving again was to spin it with a separate 12V power source. Then the extruder controller would spin it for a little while, but it would inevitably stop again (matter of seconds or minutes).
However, the motor never got hot when it wasn't extruding, which I would expect if it was trying to turn but caught on something.
As far as I know I've got the latest firmware, which implies this ISN'T the same problem outlined in the Great Motor Mystery http://wiki.makerbot.com/the-great-motor-mystery since they claim to have fixed the bug. Also, mine won't just malfunction after I press stop; it will also just not work from a complete reset (overnight) of everything.
I took the motor off of the extruder (still electrically connected to the extruder controller), and took the front plate with the bearing and the shaft off of the gearbox. Then I just sat it on the counter and watched the open gearbox turn. There's nothing in the gearbox preventing the motor from turning. I watched dozens of revolutions of the (top) slowest gear and it never stopped in the same place twice.
So, the problem is earlier then the gearbox; either the motor itself, the extruder controller, the motherboard, or the powersupply.
Now things are extra awesome. I WAS checking the leads from the extruder controller for voltage yesterday. The V to the motor varied depending on whether or not the various heaters were on, but didn't seem to drop below 10.3v. About the last thing I did last night was watch the motor, with no load on it, start, then stop (nothing unusual there) and then start, shudder for a few seconds, and stop. Now I can't get ANY voltage out of the extruder controller. The motor still works just fine (external 12V power supply), the heaters work, and the various stepper motors work.