As a follow up, I also received "ControlledAccessException" errors on a couple of third party apps after the tranport operation. These were not cleared upon a restart of the handheld, nor even when the software config was removed.

I then transported another handheld from 4.1 SP6 to 5.0 MR1 without specifying a software config, everything came over perfectly with no reset prompt, and no "ControlledAccessException" errors.

I will need to test this new fangled 5.0 application control policy (and associated apc for unlisted apps) thouroughly apparently...