Can't recreate with a clean run, and can't send a save due to both not having one anymore, and a series of private mods.
I
can confirm that it's not a result of conflicts with adjustable skill thresholds, which I thought it might of been (since I'd doubled the threshold, and the decrease was double what I'd expected).
EDIT: Have been able to recreate it, although not track down a culprit.
"adjustable_skill_thresholds",
"lw_console",
"IndEvo",
"lw_lazylib",
"MagicLib",
"trulyautomatedships"
No AI core assigned: 80 points
AI core assigned to ship 1: 50 points
AI core assigned to ship 2 (instead of ship 1): 20 points
Edit 2: Able to recreate with just the libraries, Console Commands, and this mod, so probably not a conflict.