I also run Firefox in Xephyr - on debian 32bit. I _often_ have had the capslock or shift get stuck, and I too always had to restart Xephyr.
IIRC it always got stuck when I alt-tab away from (or back to) Xephyr (maybe because I hit the shift key accidentally? or maybe the capslock was on? ) I hope you can find an answer; please let me know. If you file a bug, please forward it to me &/or send me a link. Thanks Charles