MakerBot Industries

What firmware are you running? This sounds like a firmware feature, not a hardware problem, but who knows.

I'd try going back a firmware revision on the motherboard

But wait, isn't the the power supply supposed to be stuck on via a resistor on the motherboard for the turn on lead? This means you have a short of some kind that manifiests itself when hitting the Estop. I would check and ensure you soldered the safety board correctly (for MK6+), you don't have some other short in the heater head (if running MK5 style), or possibly a short in the ABP motor or wiring. There are a lot of possibilites here, so it's pretty much check everything.