Thanks for the advice. Your setup sounds not too disimilar to mine so it is good to hear that a powered USB hub and active cables worked for you.
I got things working with a powered hub for an observing run last weekend, and I am now waiting for another clear night to see if this really has fixed the problem. I’ve found everything just works fine in the daytime, it is only when I start proper night time observing that I get drop outs! From the sound of it powered USB cables will be the way to go if I still have problems.