I have been reading a lot of the posts on ECM issues with the 1999 Dodge 5.9L Diesel. I am looking for a clue as to this new problem to add to the mix.
I had a short in my drivers seat that killed my battery causing me to disconnect the battery and charge them from time to time. Every now and then when I disconnected the battery and reconnected it I my truck would not start. No Fuel pump etc. I checked the fuses and relay to the fuel pump and found no power there, however at times when I probed it with my meter, It would activate the ECM.
Does that mean that I have a bad ECM? I checked the grounds and as many connectors that I could find. I am just not sure. I do not want to purchase an ECM and have the same problem.

 

Sounds like you are back powering the ecm thru a hot lead wire. I think the seat power is on a relay. That may be a good place to start. I am on my second ecm and at about 80K since the new one....not sure the ecm has anything to do with the accessories though....any aftermarket goodies or backyard electrician items??