Somehow the search is broken. It worked right after the installation and a few days later it stopped.
Now it only displays a link named: Use standard sugarCRM search.
We have checked the cron schedule which is running just fine. Also the logs, but cant find anything strange.
Is the AOD scheduler running?
After a long research we found that the new lucene search creates flat index files and needed proper permissions to the folder where its writing its files too.
Yep, you need to run the scheduler so AOD can index. If you do not wish to use AOD, you can disable it in Admin -> AOD Settings.