When loading the game my inventory shrank and dumped a bunch of items on the ground, including bizarrely a bunch of Mk2/3/4 spider-trons. This hasn't been a problem until now. Tried reverting to 1.1.27 but no change.
I am not (or wasn't, I installed big bags as a workaround after my original post).
Though playing with that bug I got some possibly relevant results
Entering and leaving the train returns my inventory to 12 rows, this happens regardless of if I have big bags installed (and it shrinks) or not installed (and it grows).
Should be fixed in v1.8.9. Unfortunately there's no way to change your inventory size bonus back to what it should be, so please use /c game.player.force.character_inventory_slots_bonus = 0 (replace 0 with whatever it should be for your save).