Ok, sorry for the delay on this end. Here's the stutter issue in more detail:
If you do whatever is required to get to the point in the screenshot, this of course triggers the 'copter. You'll be on the Neuroscience rooftop, prior to entering, meaning the 'copter is shooting RPGs at the player. Once it starts firing RPGs, each time it explodes there is a momentary stutter. That stutter starts at the instant the explosion is heard, and lasts for maybe around 100ms. Very roughly - it's short, but there.
You can see this by looking at the tile immediately to the right of the crosshair in the attached screenshot, This tile flashes quickly, and is at the top of one of the columns, in front of the force field controlled by the yellow keycard. This (very) briefly stops flashing, when a RPG explodes.
You can also notice this by moving around up there - there's a noticeable stutter in the screen refresh, at the exact moment of an RPG detonation. That might be easier to detect.
I simply DNKROZ/CLIP/STUFF and fly up there. Edit: I avoid the main sector in that area that triggers the first truck, to make things simpler.
Here's where it gets a little weirder: if the player jumps down to the yellow keycard, or jumps down to the courtyard with the fountain, this stutter goes away, until you get back up there.
Anyways, just in case it's germane, I'm rockin' a 10yo-ish Thinkpad Helix 2, which uses a fanless/heatpipe Core M-5Y71 CPU @ 1.20GHz on Win10/64 (I think it actually goes to 1.4Ghz) and 8Gb of ram. Big whoops, right! What might be notable is since this is a resource constrained system, the stutter is more noticeable.
I'll try defeating the 'copter there next (massively cheating of course) and seeing if there's a noticeable frame rate issue, that depends upon being on the upper level vs in the courtyard. It'll be a few days while I travel but I'll get some idea of whether being up there causes framerate issues during the end of that battle.
Edit: No DukePlus whatsoever, and this is a very recent eduke32 build. I also copied the DukePlus eduke32.exe to a fresh directory and tested the same scenario, and the stutter happens with that one too.