Pete,
I posted this question on the SimJet help forum:http://www.rcuniverse.com/forum/m_2939082/tm.htm

I have a Triton also and never had a problem. When I got the note from SimJet that you could cook the ECU by charging through the charge cord, I started disconnecting the battery before charging, as per SimJet's instructions. I would think if there was problem with my setup, I would've cooked it the first time I charged the battery.
As great as the engine and GNM are, it just seems a like Mickey Mouse way of charging the battery. I would think that a workaround wouldn't be that difficult, but, guess so.
BRG,
Jon