I'm having a different problem - the auto-throttle doesn't do anything at all sometimes. It still sets its targets correctly, but it doesn't seem to be able to actually control the aircraft's throttle. It's very strange. And yet, sometimes it does work. Has anyone else seen this?
And now, after posting that, I'm having an even stranger problem.
Airplane flying along at 380 m/s. 2/3 throttle (it's a fast plane). I push the target speed up to 440 m/s... plane throttles up a little bit, starts accelerating, then throttles back and the acceleration falls back to 0.1 m/s^2... and stays there. Slooooooowly accelerating. Nowhere near max throttle. Acceleration target is shown at 10 m/s^2, and it's not even trying to do that. Even in the brief acceleration after i bumped it up it only accelerated at 2 or 3 m/s^. Again, plane is nowhere near max throttle. It is definitely capable of the target acceleration, it just isn't throttling up.
If I set the speed DOWN, it will throttle all the way back to idle to slow down, though!
I reset the PID tuning to defaults just to make sure I hadn't caused this somehow. Still the same behavior.
I'm baffled.
EDIT: Figured it out. It was another mod that had a setting which I knew existed but didn't realize was enabled. I must have accidentally turned it on at some point and forgotten about it. (If anyone else runs into this problem, make sure you don't have "Limit Q to [value]" enabled in MechJeb. I probably would have thought of that sooner, but I never use that setting so the idea that it could be turned on didn't occur to me).