nah, it doesnt pause during downloads Robin.. It may be single thread, but it doesn't do that.. The USB bus can handle the information coming down from the imager and the guider at the same time, not to mention the guider is only downloading a tiny sub-frame, guide pulses sent to the mount via the camera are tiny little bits of information too.. It wouldnt require 2 threads to complete the tasks...
I had maxim guiding and downloading an image about 15 mins ago before this cloud rolled in
good looking sub of NGC253 it was too..