I was at .916, updated to latest .931 just now and did a test again.
Testing with the game Pang, boot from adf, set up as A1200, kick 3.1.
Launching the game with the USB pad inserted joysticks in Game1 and Game 2 port.
After the game is started I am able to get one joystick to work, but as player two only. Activate the other joystick and it will take over as player 2 while the first joystick gets inactive. I can do this both ways, to toogle the player 2 control between my two joysticks.
Now doubletapping the USB pad and this will control player 1 and the active joystick controls player 2.
Then if I unplug the usb pad while in the game, neither joysticks will work afterwards.
I can off course make changes in the controllers setup each time before launching a game. And set one DB9 input to port 0 and the other to joystick, but since this is a global setting it means the system mouse settings for Amibench and other setups will be affected as well.
If it was possible to have change the controller settings for each game it would be easier.