Terrain elements, including square tiles and floor pipes, will occasionally flicker in and out of shadow.
I have observed this behavior both before and after the major update on 4/25. I haven't encountered it since the updates on 4/27 and 4/28, but I also didn't play very much between 4/26 and today. The flickering doesn't appear to respond to my mouse and keyboard inputs. I am playing on a MacBook Pro running OS X 10.6.7; I have no idea whether my video drivers are up to date, as I don't know of any way to manually update them on a Mac. My graphics card is an NVIDIA GeForce GT 330M, and my Intel Core i5 apparently has a built-in "Intel HG Graphics" GPU with 288 MB of VRAM. I play Spiral Knights in windowed mode with a resolution of 1024x768x32 0Hz and the graphics quality set to low, vertical sync enabled, and other advanced options disabled. I am happy to provide whatever other relevant details are needed to diagnose this bug.
Screenshots: http://img849.imageshack.us/img849/391/shadowbug.jpg
Are you running on a MacBook Pro model that was released in early 2011? Then you could try giving this update a try. Other than that there seems to be no driver support outside of Apple for your device.
I used to see those kind of errors on two different Windows computers, but correcting the drivers has since gotten rid of them.