I've done everything short of formatting and reinstalling windows. Earlier today I removed everything, uninstalled x3 tc, and deleted the install folder. Then I reinstalled everything including Lucike's scripts. Only thing I couldn't get rid of was the X3 Plugin Manager (no uninstall yet). I started a new game and used the cheats/SETA to re-setup the test.
The result was the same issue. Its my machinist this time. The navigator and helmsman that boarded the ship at the same time are working fine.
Not sure if google translate/I'm reading this correctly but this seems to be the same problem:
xuniversium forum
Update: I did some more testing on this to see if another crew member was somehow blocking the machinist's improvement. I don't think it is. I stripped down the crew completely, then left only the same navigator, helmsman and machinist. I ran SETA for 10 minutes and both the Nav and Helms started working, the lazy machinist didn't.
I then switched helms, machin, and nav's jobs around. The Machinist who is now a navigator is still refusing to do his job. Switched them again with the buggy person as helmsman, same issue. The control variables (nav and mach) worked fine. I finally transferred the bugged person to a carrier as a recruit, stuck them in a cockpit and they registered as Tracy Fisty-N, i.e. navigator. Clearly some part of the script understands that she is trained as a navigator even if she refuses to do the job.
Really seems like the problem is with the retrain marines/change occupation functions, for some reason with some marines, their new job just doesn't stick.