Just a quick follow-up: I can use the suggested workaround as follows.
1) Create a bash-script in my homedir with the xmodmap command.
2) Add this bash-script to startup applications.

It just didn't work when I put the command directly in startup
applications... Go figure..

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https://bugs.launchpad.net/bugs/1072120

Title:
  ~/.Xmodmap not read on login

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