I just tried to take some snaps with the lens cap on in manual mode (F10, exp 1/80, iso=100, EV=0 in case it matters).
-When in auto-focus it wouldn't take a shot.
-When either the camera or the lens was set to manual it then snapped, both with the shutter release button on the camera and the remote.
-Didn't seem to display the 'subject is too dark' when I was taking the blank shots, but it did flicker on briefly a few times.
That all makes sense, so that is good. Shutter and aperture priority should work the same way.
Does it matter whether I turn the auto-focus off on the lens or the software?
yes, see eyelight's post
Could this be anything to do with the AE-L/AF-L function? I tried to use that the other day but can't seem to get the hang of it/not quite sure what it does. I've worked out how to set how it functions, ie. hold down or one click, but whenever I try to use it it just seems to do the opposite of what I think it's doing....
You don't have those focus/release priority modes that Paul mentioned.
If you messed with the ae/af lock, that could mess you up a bit. You can't fully do the 'back button focus technique' on the d3200. That is because there is no release priority menu setting. So if you change the behavior of the back button to 'AF-on' and then recompose, the shutter may not fire because the focus point is not satisfied. I would set that back to ae/af lock for now.