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.