Yeh, its not linux related.

If you have the keystrokes, alt+1, ctrl+1, shift+1, assigned to other actions, the ones on your action bars won't go off

Edit: Alternatively u could make the macro /cast fireball [nomod]; [mod:alt]; [mod:ctrl]; [mod:shift] and i'm pretty sure that'll make it do nothing when u press the modifiers, i'm not well versed in macro making though.. could be wrong.