I don't have an answer on how to fix it (I don't own IXS and, from my experience, it's a struggle to get any games from the early 2000's to recognise controllers/controller input, even if you're using a Logitech controller from around the time of the game's existence), but I just wanted to add...
...if you're okay with using the controller to input keyboard presses (not great for joystick movement, but still) you could also try Steam's "Big Picture Mode".
Steam's "Big Picture Mode" is compatible with most console controllers, and - by using "Add a Non-Steam Game..." to add IXS' .exe file to your Steam Library - you can boot the game up in Big Picture Mode and change controller bindings on-the-fly by opening the Steam Overlay and selecting "Controller Configuration".
Perfecting the control bindings does take quite a while, but you can pause to change them any time, save and load controller binds, and the configuration screen has various options for defining controller input (so if you can't fix directional movement you can probably fake it by applying keyboard binds and fiddling with Joystick/Direction Pad settings to make it slightly less janky. It'd be rough as hell, but it's better than no movement at all).
Regardless, I wish you the best of luck in finding a solution that works well for you.
...also, welcome back to the fourms, Mysteli.