I jumped onto the IRC thing and Lax and Stealthy helped me out. It turned out to be a very simple setting, the 'Hold' option needed to be 'On' in order for the keypresses to get passed properly.

I think that using the keyboard shortcuts will really make a difference to multiboxing EVE, it allows you to do stuff like (un)docking, jumping at gates, etc without clicking on each client or using mouse broadcasting (which I find unreliable)