Can you do something similar with specific parts? I have found that on several mods, the ATM will be fine on all of them except a few, but with those, it stalls, semi-indefinately. I have found this with Chopshops impellor, several of the rocket bodies and the aerospike engine from Sounding Rockets, the F1 engine from a saturn mod(?), and probably a few others. Once I remove those particular parts, everything works fine.