1-Have a 'main ship' with a command disc
2-Have a 'subship' on an interstage with a command disc, off by default, you need to start an activation group to power it on.
3-have a simple program run on the subship.
Test 1: launch, detach and activate the subship, the program should run.
Test 2: launch. Quicksave, quickload, detach and activate the subship. The program will NOT run.
I found the same issue if you save the flight and return to it. It's as if the 'paused' state of an Onstart program isn't saved properly when loading, and power is off for the command disc and it's not a currently active command disc. Just my theory.
Still, it is desirable to carry subships such as rovers, keep them offline until needed yet still have working programs.