When swimming submerged in water changing from Combat Pace to Jogging does not affect speed of swimming, however it makes a significant difference to your stamina usage. In one case you lose stamina at an alarming pace, in the other, you regain it as if you were not moving at all.
While I haven't checked; I suspect this would apply to swimming on the surface of the water too.
Spawn as a Diver unit.
Toggle between Combat Pace and Full Speed while swimming fully submerged.
Observe Stamina Drain.
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.