You can lock the framerates enabling v-sync or playing with the video drivers.

Now when you say "uninstalled" did you completely wipe the folder clean? Even if you do a quick-uninstall via steam it leaves your RSRC files and a lot of other things.

This seems to be a case of corrupted textures/missing textures and they aren't properly redownloading. Verifying the Cache in this case doesn't check the RSRC Folder. In fact, I deleted an entire folder and the Cache verified the Game without even replacing the files.

Your Sprial Knights Folder is in ...\Steam\Steamapps\Common\Spiral Knights\ ensure that you COMPLETELY DELETE THIS FOLDER and then try reinstalling the game.

The Lag most likely comes from the game trying to constantly access textures that are either corrupted or are missing. When I removed a song (Back when I used to run FSC with my alts) I used to gain massive FPS drops on my alts and perfect framerate on my main, once replaced my Framerate shot back up for all clients. If anything, try updating your drivers.

Glad to see this worked.

As for what causes it to happen? No one knows and the most you can assume so much. Could be lag and missed a file, could be more, I don't know and as for as I know, no one does.

I've never had this happen in my two years of Spiral Knights so I just count myself lucky I guess.

How can you possibly tell that you have 180 fps? The game doesn't have any sort of counter, and there's no way you could tell that with the human eye.