LB7 to LLY Swap ECM Bootloader error

The truck is up and running great with the stock ECM tune after a VATS Re-learn. If I try and retrieve the stock tune I get a bootloader error. I also get the same error when trying to do a DSP-5 full flash. So far I have noticed that the LB7 fuel tables need to be in the LLY ECM (im gaining fuel as I drive). The other problem I am having is with the factory alarm. If the remote is pressed to "lock" the truck twice, the alarm geos off lol... Any help with getting into the ECM would be great, thanks EFI crew!