I usually play this game through Steam, fullscreened. If, while I'm in-game playing, I open the Steam overlay (which I do regularly to check stuff on the wiki), and I then minimize the game, it locks up. I won't be able to de-minimize it, it just stays there stubbornly in the task bar. The only thing I can manage to do is close the game and start it right back up again.
This isn't a question of chance; it happens every single time I do this, guaranteed. I don't think it's a problem with the Steam overlay itself, because I can minimize other Steam games with the overlay open and have no problem. It only happens with Spiral Knights.
I've noticed this too, im not sure wether or not its your computer or not, but it happens all the time on my mac.