There are two modes of operation with the software :-
Block Mode - ns/div up to the "Collection Time" which by default is 200ms/div
In this mode the scope captures data to it's internal memory before transferring the data to the PC. The trace is not updated on the screen whilst this is happening but is drawn on completed collection of the block.
Streaming mod - from the "Collection Time" up to 5000s/div (nearly 14 hours)
In this mode data is streamed directly to the PC and not stored on the device. The software will read this data and draw the trace live.
I believe that when this transition occurs your PC is struggling to keep up with processing the data and drawing the trace and due to this the scope loses connection with the driver.