With the last update we made to the software to allow the full reflashing, the additional data that is gathered (as mentioned above by John) is only so a complete operating system can be transferred to another ECM, all the normal calibrations from a truck have always been read out so it should not matter if you have an old or new file version.
I would suspect the two primary reasons it's not working is either -
1 - One of the emissions related DTC's being set.
2 - VATS not learnt correctly.
With the new ECM, did you just plug it in the truck and it ran?
Something you might want to try with the new ECM in the truck.
In the tune tool go to the System section, then VATS.
Make sure G0301 is set to 'Enable'
Set G0302 to 30 (seconds).
Set G0304 to 1
Then follow the proceedure in the description for G0302.
I can't gaurantee this will work to fix your problem, but certainly on the gas ECM's this is something that must be done to learn the theft codes on a new ECM, but normally they will not even start without the relearn proceedure being done.
I also looked through the TechII menus for VATS relearn on the LMM and could not find anything, which confuses me even more!
I have also added in a few new PID's to the scantool to show the reasons why the remote start was disabled, these will be in the next update (due this week).
The only advantage in getting the dealer to reflash the new ECM is the tune that will be flashed in is 'exactly' the one for the truck, but, if you already have a copy of he's stock tune then there is no advantage in visiting the dealer now EFILive will do a full reflash on the ECM.
We'll figure this out soon enough I am sure.
Cheers,
Ross