Essentially, my military will act like they are civilians. Whoever I assign, from what I can tell. The members of any squad, new or existing, will run away from threats, perform civ jobs, and will appear as whatever their profession icon is, ie farmer. Their ames also do not appear in bold in Dwarf Therapist, even though they are listed as in a squad. Schedule is set to Active, but even changing that has no effect. Have switched equipment, dorfs, barracks, armour stands etc to try to alleviate this, to no effect. Most related issue I could find was for vanilla, and appears to have been resolved by Toady: http://www.bay12games.com/dwarves/mantisbt/view.php?id=1617

I have an inkling that previous events may have caused this - I accidentally breached the third cavern and forgot to wall it up. Floating brain came up, started a fire and got killed by my then-military-commander (He did "look confused" in the battle logs). After that point, my commander went round and killed some people, and everyone was fighting/paranoid, before he got impaled by a miner. Since then, the military hasn't worked. (v4i)

Edit: They appear to act as militia when given a direct order, ie station or kill, but only for the duration of that order