Hi Richard,
sorry to hear about your troubles! We had some reports where X-Plane key mapping went south - for example people reported that the B key will not only apply brakes, but also toggle the Beacon on and off... I think it is an X-Plane quirk, remapping usually helped.
If you get a gizmo-soft-crash (window pops up), the code has failed. At that point we would love to get the gizmo_log.txt file and the IXEG_FMS_debug.txt files (available after next update to 1.0.6) from you, so we can find the reason and cure the crash. After that event, the code will not work right, anymore, and your best bet is to continue with conventional navigation (like you did).
1.0.6 is pretty imminent, and I would suggest waiting for that one before you go through the trouble of reporting any further code-crashes, that one should fix up quite a few of those again.
We don´t have plans to add the older "paddle" type AP panel at this point - the current combo (new panel, steam gauges) is in use in real life, and the old panel with it´s constant clicking of the lockouts would drive people nuts .
Cheers, Jan