Hmm, that's pretty bizarre. Have you tried deleting and then re-creating the virtual joystick? And just using UCR to map the buttons/axes? And can I confirm that you've tried to run this in Freespace using Knossos and the buttons/axes don't work?
Alright, spent a while trying this, disabling and re-enabling, and I still can't get it to work. I've also tried enabling a second vJoy and forcing UCR to use it, instead of vjoy1. No go. Running UCR with admin privileges still no go. I tried using ViGem, and UCR can send the information quite well to it.
ViGem is not ideal, as in other games, like Darkstar One, it has a deadzone the size of texas, but it works well on Freespace. A workaround until I figure this out, since it has limited buttons and limited axis.