Hey Fellas, I have an update on this one.
I had another report of this via tech support yesterday, so I spent several hours looking into the problem. As best I can tell, the flight plan is not synchronized with the GNS 530 when the GPS is hot-swapped in by my code, which can sometimes happen right after the aircraft is loaded. Clearly, other GPS units do not have this problem, so it should be something fixable in the GNS 530's code. I spent way too long trying to find a solution last night, so today I will write to some of my GPS developer friends for advice. Hopefully we can have a solution for you soon, and I can encourage Working Title to include that in SU15, before the release of my Dukes.