My throttle on my joystick works fine in flight assist mode does not work when F/A is turned off. The throttle worked yesterday for the physics mode not sure what happened I have not changed anything since loading the game yesterday. My OS is Ubuntu 11.10, joystick is a Logitech extreme 3D pro, and I am running all of this on a dell laptop.

Odd, I don't know why it would mess up, unless you changed what controllers are plugged in - doing that can cause the joystick to be assigned to a different device file, which makes vendetta forget its configuration. I use udev rules to force my controllers to always have the same device files in order to avoid those sorts of problems.

Try binding the JS throttle not to "throttle" but to "accelerate". But that probably won't be good if you want to switch back and forth between FA and physics.

http://www.vendetta-online.com/x/msgboard/1/25034?page=3#309151

Most people who use physics mode don't bother with the throttle though. I have the same JS as you. What I like about this model is that the hat switch is centered nicely. So I use the hat for accel/decel, and I use my left hand on the keyboard (technically a Nostromo n52, not a real keyboard) to strafe. I don't like the buttons on the base of the joystick, and only use those for auxiliary things (hailing, pining a target, cargolist, etc.). I don't use my throttle for anything.