I've had a longstanding annoyance, which I thought was a bug in rxvt-unicode. In several reproducable situations, I would not be able to type in the terminal, despite it having "focus" by the window manager. After gnome-screensaver is unlocked, or after exiting Firefox or OpenOffice with the focus back on rxvt, no input was accepted by the terminal. Switching to another workspace or application and back fixed the problem, so it was annoying but not world-ending.
Xterm did not suffer from this problem, so I was sure it was a freak rxvt thing. I filed a Debian bug last November and then let it sit. Just recently, they marked it as non-reproducable so I got more serious about figuring it out. I started from a fresh account and gradually added in my old configs and settings until I was able to reproduce the problem. Surprising (or not so surprisingly if you read the title of this post), scim was causing the problem.
What seemed to trigger it was running
im-switch -s scim
This was creating an xinput.d directory in my home dir, and symlinking some config files for "scim" mode. After some investigation, I discovered that there were other "modes" that scim could run in. I also discovered there were other programs to set up xinput, such as im-config.
After playing with a few modes, I found that a 'scim-bridge' mode fixed the problem. It apparently has something to do with incompatibilies with C++ abi versions or some such thing.
I actually switched to using im-config and set it up in "auto" mode, but that appears to be running scim-bridge mode too.