First: Thanks everyone who took the time to look at this.
The issue:
The engine stutters, so I just have to do all the nodes by hand rather than relying on Mechjeb, which sucks.
Repro:
I can get repro with just Mechjeb - although the whole thing shakes so much, so I added KJR.
All mods for repro:
Kerbal Joint Reinforcement - Next (KerbalJointReinforcementNext v4.2.27)
MechJeb 2 (MechJeb2 2.14.3.0)
Module Manager (ModuleManager 4.2.3)
So here's an image of the ship that does this engine stuttering when I have Mechjeb control a maneuver node:
https://steamcommunity.com/sharedfiles/filedetails/?id=3306126647
If I hit space bar to get rid of the bottom tank and engine, so that the only remaining engines are the 2 near the top of the ship, the problem continues to exhibit. Those engines seem to be why it stutters when Mechjeb is controlling the node execution for some strange reason.
Remarkably, this design also stutters:
https://steamcommunity.com/sharedfiles/filedetails/?id=3306144338
So much for my hypothesis (I had wondered if maybe it was because the original design's engines might not be precisely aligned, but these should be pretty close to exactly aligned).
I think my takeaway is that I'll just have to test every ship design using cheat-mode to make sure they work okay with Mechjeb before using them on missions.
Workaround:
I found that moving the engines to the bottom of the ship caused the stuttering to stop:
https://steamcommunity.com/sharedfiles/filedetails/?id=3306565772
That's kind of a shame, in that I had them at the top to work around a stability problem and I thought they were fine up there. But it seems if I want to use Mechjeb, then I'm left with no choice. It's an interesting bug, but I think no more development is going on for the Mechjeb mod. Nevertheless I might post this thread as a duplicate into the Mechjeb threads. I'm not sure where I would post that though.
