My staff slots go into the fatigue object for a soldier and simply reduce the number of hours needed for recovery. In particular, I do not start any kind of project or anything when a soldier is slotted like literally every other staff slot does.

The way the slots work, a soldier is technically put into the slot when you simply mouse over their name in the choice list (This is the bug and I don't understand this decision at all). Not when you click on them. This normally doesn't matter because the staff slot project doesn't start until you make a choice. The hassle becomes that I don't use a project to adjust the fatigue times.

The problem is then that soldier fatigue times are all just reduced by mousing over their name. To fix this, I don't actually touch any fatigue times until you leave the living quarters. Then I go through all of the slots and reduce the fatigue times that I need to based on who is actively taking up the slots.

This means though that I can't actually tell who is in a slot until you leave the living quarters and thus can't update any kind of text or message boxes or anything.