Were you heating the bed too, or just the hot end?

Do you have a print cooling fan that is set in the slicer to kick in at say, layer 2?

I'm just wondering about a possible thermal runaway situation. The OEM builds from MakerFarm at least up to some point had thermal runaway detection disabled. There was a thread here some months ago where an early adopter of the revamped Marlin started getting thermal runaway errors when he upgraded to it. It turned out that at least as of that build, the default was for thermal runaway detection to be enabled. If I recall, that problem was with the heated bed - it would heat up OK but then in the print the bed temp would drop off just enough and for a long enough period to trip the thermal runaway condition that shuts down the print. I imagine the same thing could happen with the hot end if too much print cooling airflow is applied after the hot end is at temp and the heater can't keep up with it.

EDIT: Reading tsteever's latest post that came in while I was typing, this sounds like a real possibility