I had the same problem on my Xubuntu 12.04 too, but only for new created
accounts, not for my existing one. After some hours of trial and error
I've got the one file, which made the difference: It was
~/.cache/sessions/xfce4-session-MYCOMPUTERNAME:0 . So simply saving the
desktop session once solved the issue for me.

The hole problem and the solution/workaround is easily to reproduce, at least 
on my machine with Xubuntu 12.04:
1. Create a new user account with an completly empty home-directory.
2. Copy the .Xmodmap file to that home-directory.
3. Log in. There will be a lot of files automatically created, the .Xmodmap 
file will be read in and Xorg will run at 100%.
4. Ignore what Xorg is doing and go (under XFCE) to Main menu -> Settings -> 
Settings -> Session and Startup -> Session -> Save session.
5. Wait until the session is saved, log out, log in and everything is fine. The 
.Xmodmap is read in, but no Xorg running at 100%.

Notes:
- Maybe you have on an existing account also to disable the 
xfce4-settings-helper in Main menu -> Settings -> Settings -> Session and 
Startup -> Application Autostart, but I'm not sure about that.
- When I manually read in the .Xmodmap with the command "xmodmap ~/.Xmodmap", 
there will still be 100% CPU for about one minute, both in the existing and in 
the new account. But because I do not need to read it in manually, this is, at 
least for me, no problem.
- Debian seems to have the same bug, see 
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=687112 .

** Bug watch added: Debian Bug tracker #687112
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=687112

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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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