2006 Ram 2500 CTD advice needed

ECM is the engines computer which is mounted on the drivers side of the eng block. It gets power from the fuse block next to the front of the eng and it gets ground from a bolt that has several wires connected to it at the edge of the quarter panel on the drivers side.
I really think you still have a connection issue. You could trace some of the wires (including grounds) that start from the battery connections and go to other places. check both ends for looseness.

Also, and this is a stretch, do you have a factory security system with coded key? If so then maybe try your other key.

ScottG wrote:
I did a little searching and found another 06 where the same exact thing happened after unhooking the batteries. I his case a small ground wire was left slightly loose (just touching) for the ECM.
So make sure every connection is tight especially the smaller ground wire that goes to the edge of the qtr panel on the drivers side.

OK, I'm going to go out and undo that bolt and reverse the order to see if that makes a difference. I have the other wire (which you have mentioned for ECM) against the qtr panel, ground wire from battery, and head of bolt. I will retightened this. If that fails I will try ground wire from battery next to qtr panel and see if that makes a difference.

Rechecked all the ground wires and cords to make sure all appropriate wires were included when hooking up new batteries. Nothing looks missing. In fact, didn't even take bolts off at terminals, just loosened and slid off so as not to lose any connecting wires. I did get the correct batteries, 65S.

Tried to do the on-off-on-off-on thing quickly but got no codes. The check engine light just blinks rapidly and I hear a loud clinking sound, not like you get with a dead battery. This clicking is happening when I turn the key in the on position b4 I get to the cranking position.

Also, not sure what you all are calling the ECM. I don't know exactly what that stands for. I'm not worth much under the hood. Thanks for all of the help so far.

I did a little searching and found another 06 where the same exact thing happened after unhooking the batteries. I his case a small ground wire was left slightly loose (just touching) for the ECM.
So make sure every connection is tight especially the smaller ground wire that goes to the edge of the qtr panel on the drivers side.

Check all fuses and make sure that all the cables were re-installed on both batteries. I seen a guy accidentally leave the charge sense wire off the drivers side battery once. The actual charge wire from the alt is on the passenger side battery. The computer didn't sense any power and sent full charge power out which melted the battery to the point it was boiling out of the case.

Check all of the ground wire connections at the batteries. The ECM has a dedicated ground coming from the battery. If that connection is lost it will crank fine but will not start and the engine light will flash.

Cycle the key on-off-on-off-on within 5 seconds and the codes will be displayed in the odometer. You will certainly have a code that says the ECM lost power but there maybe others as well.

Most likely has codes. Have it scanned. I'm betting it lost it's smart key programming.

Never seen that condition with any 3rd gen. Sure all he battery connections and cables are good? Wish I could help. Good luck!

Assuming you replaced both batteries with the correct size (#65s) make sure they are fully charged. The engine must turn over fast enough to generate the minimum fuel rail pressure (somewhere around 5-6 thousand psi). The ECM senses this pressure and will not start to energize the fuel injectors until the minmum pressure is reached.