Several times while in the middle of a battle, my attack/action buttons have become unresponsive. This has resulted in my totally getting murdered and losing stuff, and having difficulty activating any of the menu buttons as a result of the key bindings. I've tried switching up the mouse buttons from left to right and vice-versa, but it doesn't seem to be a hardware problem (e.g., broken mouse button). The keyboard keys seem to be unaffected, though, it's just the mouse input that dies every now and then.
I'm running Spiral Knights on Ubuntu 10.04 32-bit.
There are already a number of other threads about input issues and Ubuntu. Have you tried the suggestions in those threads?