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a60fb26
(Get the code!)
Here's an update. After a few days of running GNOME, the same problem occured again. Apparently the problem is not caused by Unity!
Meanwhile, I found some lines in the logfile:
May 17 11:47:48 zenbook rtkit-daemon[1691]: The canary thread is apparently starving. Taking action.
May 17 11:47:54 zenbook rtkit-daemon[1691]: Demoting known real-time threads.
May 17 11:47:59 zenbook rtkit-daemon[1691]: Successfully demoted thread 2257 of process 2250 (n/a).
May 17 11:48:16 zenbook rtkit-daemon[1691]: Successfully demoted thread 2256 of process 2250 (n/a).
May 17 11:48:37 zenbook rtkit-daemon[1691]: Successfully demoted thread 2255 of process 2250 (n/a).
May 17 11:48:45 zenbook rtkit-daemon[1691]: Successfully demoted thread 2254 of process 2250 (n/a).
May 17 11:48:55 zenbook rtkit-daemon[1691]: Successfully demoted thread 2250 of process 2250 (n/a).
May 17 11:49:02 zenbook rtkit-daemon[1691]: Demoted 5 threads.
May 17 11:49:12 zenbook rtkit-daemon[1691]: The canary thread is apparently starving. Taking action.
May 17 11:49:16 zenbook rtkit-daemon[1691]: Demoting known real-time threads.
May 17 11:49:20 zenbook rtkit-daemon[1691]: Successfully demoted thread 2257 of process 2250 (n/a).
May 17 11:49:29 zenbook rtkit-daemon[1691]: Successfully demoted thread 2256 of process 2250 (n/a).
May 17 11:49:52 zenbook rtkit-daemon[1691]: Successfully demoted thread 2255 of process 2250 (n/a).
May 17 11:50:22 zenbook rtkit-daemon[1691]: Successfully demoted thread 2254 of process 2250 (n/a).
May 17 11:50:28 zenbook rtkit-daemon[1691]: Successfully demoted thread 2250 of process 2250 (n/a).
May 17 11:50:39 zenbook rtkit-daemon[1691]: Demoted 5 threads.
May 17 11:50:47 zenbook rtkit-daemon[1691]: The canary thread is apparently starving. Taking action.
May 17 11:50:55 zenbook rtkit-daemon[1691]: Demoting known real-time threads.
May 17 11:51:02 zenbook rtkit-daemon[1691]: Successfully demoted thread 2257 of process 2250 (n/a).
May 17 11:51:07 zenbook rtkit-daemon[1691]: Successfully demoted thread 2256 of process 2250 (n/a).
May 17 11:51:13 zenbook rtkit-daemon[1691]: Successfully demoted thread 2255 of process 2250 (n/a).
May 17 11:51:32 zenbook rtkit-daemon[1691]: Successfully demoted thread 2254 of process 2250 (n/a).
May 17 11:52:05 zenbook rtkit-daemon[1691]: Successfully demoted thread 2250 of process 2250 (n/a).
Therefore I tried to disable rtkit-daemon (sudo rtkitctl --exit) and since then the system runs fine.
Not sure yet, but I believe the problem is caused by rtkit, not unity!