Hi Wiktor,
manufacturing tool expects the processor without flashloader (see chapter 5.7 in user manual). It is recommended to reset the board/processor before you start the manufacturing. Manufacturing is optimized for production (provisioning of empty devices), so there is no test whether the flashloader is already running or not.
Another potential issue: If you initialize connection at certain communication speed (9600baud), the processor does not support changing the speed without reset. So again, it is recommended to reset the board/processor before you start the manufacturing.
In the manufacturing tool, there is "Test connection" button. I can see on your screenshot, the test was not used. I recommend to use it to check the processor is connected properly.
If this does not help, please update the screenshots to show the problem. Also please test connection in Connection dialog and let us know, whether the problem is related to manufacturing only.
Regards,
Marek
NOTE: If you find the answer useful, kindly click on [ACCEPT AS SOLUTION] button