I was just now in a castle level in the Clockworks when I needed to look something up on Google using the Steam web browser. So I opened it, searched for what I needed, switched windows to see something else on my computer, switched back to Spiral Knights, and the Steam overlay was gone and I wasn't able to move around so I got killed by a very weak ghost cat.
The weird thing is, when I was trying to move around at first, I figured out I was able to move only if I was carrying a vial (poison, shock, etc.) and once I threw it I couldn't move again. I also couldn't use health items. I could switch weapons but it wouldn't play the animation, it would only show that I did on the HUD at the bottom (I couldn't attack either).
I was thinking this might just be an issue with Steam, so if it is, sorry for wasting valuable internet space. :P