I've got a laptop running Ubuntu 11.10 with the most recent updates and an Apple Wireless Keyboard that syncs via bluetooth. The Ubuntu box is also a Synergy server, using QuickSynergy to run Synergy. I'm using xmodmap to swap the option and command keys, but nothing else.

Throughout the day, windows that are long running will just stop accepting input. For example, I leave gnome-terminal up and running almost 24 hours a day. If it sits for a while, it just stops accepting input. It doesn't matter if I'm ssh'd into another machine or sitting on a local tty session, it just stops accepting input. If I open a new tab or window, those work fine. The 'broken' tabs stay broken.

I'm also running Turpial (a Twitter client) which will do that same thing. I tend to use the arrow keys to navigate, and it just stops accepting input. Closing it and reopening it causes it to work fine.

I don't seem to have the problem in Chrome, but I tend to open up new tabs when I go somewhere instead of using existing tabs.

I've updated all the packages, rebooted, and the only thing that seems to cure it is if I type on the built-in keyboard, the window will start to accept text from the bluetooth keyboard (until it stops again). I don't think the keyboard is disassociating from the laptop because it can happen while I'm using the keyboard, it seems more linked with windows that I sit for a long time. As an example, I'm typing in Chrome with the bluetooth keyboard but I have a terminal window that won't accept input.