Thanks for your answer! Meanwhile i found another thread, where a user had a similar problem.
I tried the solution from this thread (connecting the patch cable shielding to ground, rather than connecting ground from EM540 to the USB converter ground). It seemed to help, but i had one connection loss during the day. May be due to insufficient connection to the patch cable shielding, i will try to improve that by soldering).
For me, it is still strange why this happened after half a year. Nothing has changed on the system, before it was perfectly stable, now it seemed almost impossible to make it run for a while.