*Isaac drops from sky in green crate. Jumps out. "Hello!!"

Tech stuff:
OS: Ubuntu 10.10 desktop
Controllers: PSX adapter with 2 controllers
Past controller compatibility problems with all other games, which includes emulated Windows and native Linux games: None; this is the first.

Back story:
First of all, the game runs great on my 1Ghz 1GB netbook! A+ Cortex Command! Everyone I show it to wants to buy a copy. However, I can't show off how natural it is to play the game with two Sony brand Playstation 2 controllers with the analog joysticks activated. The first time I played the game at a friends house we used my adapter and the two controllers and there was no problems, so I think there could be a missing Ubuntu software repo item the game wants, but I can't tell what, exactly. Any help on this will be greatly appreciated, since blowing up 2d zombies with a heavy sniper rifle is the most satisfying thing in the world.

Solved.

Sony brand PS2 controllers with PSX dual port usb adapter works perfectly!

Solution:
Change "Gamepad 1" and "Gamepad 2" to "Gamepad 2" and "Gamepad 3".

There was nothing actually wrong with Cortex Command.

That is pretty interesting. I wonder why that is. And whether it is cortex commands fault or ubuntus.

It's the controller and ubuntu not cooperating.
I have a logitech controller on ubuntu+wine that works perfectly fine(except you have to move the stick when the game starts to align it).