After quite a lot of effort, eventually the whole problem turned out to be a real stupid thing - something I suspected from the very beginning. Reminder: The issue was double trouble. - I ran into problems in placing a button for a second, stand -alone j-link application relative to the first one. - I had a weird problem, when clicking on the button of one application actually ran the other one.
With the help of Mary Mitchell the first problem was solved. Setting the Config option "cmdmgr_trail_output" to "no" exposed the real names of the buttons on existing ProE menus and allowed to set the buttons I wanted to the correct place The second problem of "cross linking" was found by Stephanie from PTC support. The source of the strange behavior was my mistake of compiling the different J-Link programs using the "Default Package" option of Netbeans. Actually, every program should be in its own package, otherwise classes and methods of the same name from different programs might get mixed on the "first come first served" basis. In my case it was the MenuButtonListener class that was activated from program number 1 when clicking on button 2. Setting each program in its unique package solved the problem.
My thanks to all those who invested their effort to help me, especially Mary, Bjarn and Stephanie.