Ok, I have found a number of threads including
one here on Cloudy Nights regarding vertical banding on master dark images from a QSI683 which is the same camera that I am using. It seems that this is a common issue. In my case it only seems to come into effect when I am shooting short subs (e.g. 30s) so I can work around it. It is still strange though how it doesn't seem to be apparent in the individual subs but does show up following image integration.
** Edit **
The reason that I am seeing the banding after integration is that the integration process is doing exactly what it is designed to do. It is separating out the weak signal from the background and bringing it forward.