I have a related problem on a freshly installed Xubuntu 12.10.
When I type the following commands, everything but the mouse pointer freezes 
for several minutes.
xmodmap -pke > .Xmodmap 
xmodmap ~/.Xmodmap

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https://bugs.launchpad.net/bugs/998310

Title:
  .Xmodmap file makes xorg temporarily reach high cpu usage (90%-100%)
  after resume or when coming back from tty to X session

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