Thank you for your comment, it did easier our mind a little. I must say we are still wondering as this happened (so far) only with quite small number of machines. Also it is quite strange that PackageBoot scans all the files in the F-Secure folder even though they are not running.
A different thing happened with my test machine. I have one Java application running all the time and your Java Update package did not notice it. Oracle package noticed and warned me.