Hold up - It's not a vJoy thing (trying with a hardware controller). Works fine in the test screen and in the global hotkey situation, but if used in profile override mode it doesn't work all the time (which is weird, as this is the same screen for all three places). When it works it works fine, but configuring it is a little bit off kilter. I'll check it out.
Edit - This is just on sticks 3 and 4 for this screen - sticks 1 and 2 still work fine with vJoy. Sticks 3 and 4 are having trouble no matter what (which I will fix right now).
Edit - Easy fix - just had to say that there were four sticks and not 2 from the profile options screen o_O
So, commands work for all sticks, global hotkeys work for all sticks, profile hotkeys work for all sticks but can only be configured to use either stick 1 or 2 (until just now). I'll upload an, 'unofficial' build here in a sec.