In my case, I think it was because I was using oozebane in skeinforge while at the same time allowing the makerbot's hardware to try and compensate for oozing. The net effect of which must have been that the Gcode was expecting the extruder to be running; however, because of the hardware settings, it was not. If you are using replicatorG 0016, go to Machine->onboard preferences->set extruder parameters. There will be an area titled "reversal parameters". I set "time to reverse" to 0 and "time to advance" to 0. This effectively disables the hardware based ooze control and seems to have fixed my particular issue. Now that skienforge has complete control over the extruder motor, it seems to be able to correctly adjust ooze without causing skipped threads.
Another cause might be power stability issues. Other posters here have been talking about how the heated build plate puts too much load on the cat5 cable that delivers power to the extruder. I can see how that might cause "logic" glitches on the extruder board. You could try to modify the extruder PCB to get power directly from the PSU, but make sure that it doesn't cause the z-axis to get hung up as it moves up and down. A less risky solution would be to use a "relay mod" to power the heated build plate.
Although I have gotten my machine to work fine without the relay mod, I wasn't satisfied with how long it was taking my custom build plate to warm up so I added a second string of nicrome wire. Since it doubled the amp load, I didn't want to run it off the tiny extruder board mosfet anymore. Relay contacts will probably have a short lifespan for something like this because they will arc every time it switches on. I opted to try a solid state relay that I got for free from work. I'm hoping that the solid state relay will offer a higher switching cycle count than relay contacts will. At the moment, I think I'm experiencing problems with leakage current that "latches" the relay on. The build plate continues warming up for several minutes after the extruder board switches off the relay. If I disconnect one of the output wires from the relay then re-connect it while the relay is switched off, then the build plate starts cooling like it should. I think I just need to add a resistor to bleed away leakage current. If I were using a ssr built for a 12vdc output instead of 480vac, I might not have this problem at all.
Unfortunately, if you can't find someone who would give you a solid state relay, you will find that they are more expensive than regular relays. I haven't watched the retail prices all that close, but our OEM pricing at work for a relay is $2.50 and we pay $13 for a solid state relay. Also be aware that solid state relays require a heat sink and thermal paste when used with high amp loads. At ~3.5 amps, I'm not sure if the heated build plate qualifies, but I am using one anyway. I just drilled two holes in an old CPU heatsink and mounted the relay to it using a few sheet metal screws. The passive cooling it provides should be sufficient so I did not use a fan with it. I only suggest the solid state relay because of its longer lifespan, but as you can see, it involves more rigging than a standard relay will and you could certainly make the case that the extra cost/work isn't worth the extra lifespan given that a relay will probably last 2+ years anyhow. If you use a relay socket, replacing the relay is a trivial operation too. The relay just snaps into the socket and you don't have to remove the wires.
One last fix you might try is resetting the makerbot if you see that the red debug light is flashing when you notice the problem. I don't know how or why, but I have seen my debug LED flash in the middle of a few builds. I did not see any problem with the printed part though. It doesn't seem to indicate any significant problems for me, but its worth experimenting with if neither of the above works for you.