OK, I misdiagnosed the problem above, but I think now I may have found it and possibly fixed it.
I thought that the flaps and gear worked when I spawned in the air, because I tried them right after spawning, but actually, they stopped working after a few seconds. I could cycle the gear 3 or 4 times, but then they stopped, sometimes with the gear half extended, where it then stuck. Then I found that when I start on the ground, the flaps work initially, but again only for a few seconds; there's no way to take off quickly enough that the gear don't die. So the issue is that the flaps and gear are running out of power.
The following edits to the cfg files appear to have fixed the problem for me. In flight_model.cfg, in the [CONTACT POINTS] section, change gear_system_type from 0 to 1. This makes them hydraulic, which they were in reality, rather than electric. Also, in the [FLAPS] section, change system_type from 0 to 1, which does the same thing. Again, in real life the flaps were hydraulic.
That may be all you need to do, but I also went into the systems.cfg file and made the [HYDRAULIC_SYSTEM] section as follows:
[HYDRAULIC_SYSTEM]
electric_pumps = 0 ;
engine_map = 1,0,0,0 ;
normal_pressure = 500
My gear and flaps appear to be working for the duration of my flights now. If you are having the gear and flaps problem, see if this works for you.
August