It's pretty simple actually. The patrol points are above the heads of the NPC group. thus they jump trying to get to them.

As for WHY they're up there, yeah dunno.

I don't know if you guys are serious about wanting an explanation, but just in case. The issue was this:

U.S.S. Atlas Deck 13 floor is set to 1196.9 Relative To Terrain (the reason it's an odd number is a long story). When converted to Relative To Zero that comes out to only about 1193, so coordinates set Y Relative To Zero are about 4 higher.

I set the patrol path to 1197.8 and selected Y Relative To Terrain, but the selection isn't working, so it used Y Relative To Zero. 1197.8 Relative To Zero is really something like 1201.8 Relative to Terrain. Since the ceiling was set to 1201.1 Relative To Terrain, it was actually below the patrol points.

So, the NPCs kept jumping when there was a ceiling because they kept thinking "I'm supposed to be up there!". Whereas when there was no ceiling they simply accepted that they couldn't fly and remained on the ground.

Long story short: Patrol points are incorrectly using Y Relative to Zero regardless of what you have selected.

Interesting. You have stairs on that map with different levels. How do you deal with that if Y relative to geo doesn't work?

Well, I have a ramp. I didn't have enough objects to make stairs initially.

Everything on the map is set Relative To Terrain. The lower level is at a slightly lower elevation (1191.7). Since I know what each floor is set to, I just set consoles and NPCs to be 0.9 higher than the floor, which works out so that the console is placed more or less exactly on the floor (maybe the legs are a tiny bit sunk in, but only barely).

Glad to see you got it working well and proper. Also really glad it's not a case of borked for your custom maps.