Sorry, first time doing a bug report. Let me try to address all of your points.
The Log
Here's a copy of my output_log from my AppData:
https://ufile.io/psoal
http://www.filedropper.com/outputlog
With that said, assuming that log resets every time the game launches it may not be useful to you. After I encountered the bug, I zipped that initial folder ("bugreport_KSP_BPB_qualityshrimps.7z"), submitted my initial post, removed Bob's, relaunched KSP, and kept playing. I'm not a modder but I took a look at that output_log file and the only mention I can find of Bob's was module manager noting that it was removed from the game.
The Mods & The Quicksave
Yes, I know I have a lot of mods. I suspect it may have to do with the ALCOR mod, since I was getting some funky behavior right before Bob's acted up. Specifically, what happened was I began to undock my Minmus lander (ALCOR pod, DMagic science, ProceduralFuelTanks, SurfaceLights) from my command pod (just ProceduralTanks and SurfaceLights) when the game hung up for a few seconds, then killed the crew leaving me with two unmanned vessels undocked. I'm guessing that has nothing to do with Bob's, but in any case I reloaded my F9 unnamed quicksave (which I assume is just the quicksave.sfs). When the game loads back in, Bob's freaks out and fires the remaining functions of my abort group (jettison pod, arm chutes). Removing Bob's, then loading this F9 unnamed quicksave solved the issue for me.
Questions
Bob's was added before the flight began.
No, I don't have hyperedit.
No, I didn't use cheat menu.
The craft is bigboye science IIIb.craft, specifically the lander, "bigboye science IIIb Lander" in orbit around Minmus. I assume the name is unique, unless the mod truncates the name and is confusing my lander with the service module.
Summary
"bigboye science IIIb Lander" found in the F5-generated quicksave.sfs is what you're looking for
