Thanks a lot for the fast response!
The USB indicator is green while measuring, and I connected the Joulescope directly to the computer now instead of a USB-hub. Still have the same issue 
. I think it has something to do with pausing the measurement. Because I have to measure a specific signal, first I have to pause the measurement and then add the Dual Markers for exporting the specific signal. Is that the right way to do so? Or do I need to record instead of using the Dual Markers for this purpose.