As far as the HUD issue, I examined the output from the Loader program and compared it with the entry for the CS_FA18 aircraft. I noticed that in the entries added by the Loader tool, it added two entries for the HUD, which I believe is where the problem lies.

Here is the first part of my panel.cfg prior to running the loader:

window00=Main Panel
Window01=HUD
window02=GPS Panel

Here is what it put in for the panel.cfg after running the Loader:

window00=Main Panel
Window01=Weapon Control Panel
window02=HUD
Window04=GPS Panel
Window05=HUD
Window06=
Window03=HUD Glass

What is odd is that the entries are not in order, and you see a reference to a Window06 which, when you look through the rest of the cfg file, does not exist. I modified the entries to remove the Window06 and to properly order the windows, and now the cfg file works.

I haven't played with the Loader against any other aircraft yet, primarily because I wanted to test it out against one aircraft first, in case it did any long-term damage. As it was, because I uninstalled FSX for Weapons, the uninstaller did not do the clean up of any aircraft types (which I assumed it would do). I had to manually go in and clean up all of the aircraft.cfg and panel.cfg entries that referred to Weapons. Then, when I installed the 1.01 version, I couldn't run the Loader against the first aircraft, because it thought it was already loaded (and it wouldn't allow me to use the "Remove" entry to fix it). I thus had to run the Loader against a second aircraft, which is where I saw the problems shown above. When I examined the original aircraft, I saw a similar issue: an extra Window entry in the panel.cfg.

As a result, I don't think I'll use the Loader any more, as it is too unpredictable. I'd rather manually edit the panel.cfg by hand, since it seems that's what I'll end up doing anyway (with the Loader problems).