The only thing that I can say, it's that I never been able to replicate this problem. Yes, I have seen some users reporting it, and now that I read you messsage, maybe I have some ideas.
The F/A-18 navigation is not supposed to be used together with the default FSX GPS, I never tested it in such environment. The F/A-18 gauge calls into the FSX gps.dll directly, as the FSX gps gauges do. I don't know what might happen if you use both at the same time, because this is not how one is supposed to use it. The usual workflow is to use only the FSX Flight Planner, and then interact with the flight plan with the regular F/A-18 avionics only, without using the gps gauge at all. I'd even get rid of it in the panel.cfg, just to be sure...