I finally found something that works natively in linux and it's been around for a few years called xlax. It has the drawback of sending everything to the other windows and it has to be the window with the focus, which means you could play with it tucked in the corner. Only letting certain keys through is pretty easy fix. The harder part is capturing keys from the active game window. Broadcasting is easy, it already does this.

The source code is available, in c, and easy to change giving it a huge potential to become the only native linux mutliboxer software. See http://hea-www.harvard.edu/~fine/Tech/xlax.html for details.

This find is very important to me because I prefer a ubuntu desktop to stale old windows. I only went to windows because multiboxing in linux required keyclone which started to crash constantly after a while in linux.

I know this is a very keyclone based site but I wanted others in the community to know about this. Maybe someone else will beat me to making this thing the linux version of keyclone. In any case keyclone actually did let me multibox in linux for months very nicely. Nothing else seems to work.