I finally found the problem why the readout stops after a run transition. 

In my dummy frontend the serial number was not reset to zero at run start. 
This leads to a mismatch of the serial number in the function receive_trigger_event of mfe.cxx:1247.
Which is than resulting in the problem that the function founds never a new event in all ring buffers and nothing get read out of the buffer.

Nevertheless, it would be nice that the system would tell the user that there is a mismatch in the serial number (printing a warning / error etc.). 

Cheers,
Marius