I am using the mod st_stamina (ShackTac Stamina), which creates a visible stamina bar, which is how I spotted this issue. I have no mods that affect the way that stamina works in the game.
Full list of mods (just in case)
CBA v1.1.23
TFAR v0.9.8
JSRS3 Lite
Blastcore: Phoenix
Blastcore: Skies
Blastcore: Tracers
+All current st_"*" mods.