Thanks jmacon. I increased the delay between exposures from 2 seconds to 15 seconds. I was then able to do a run of 25 flats without any issue. I then tried to get cute and drop the delay to 10 seconds. SGP crashed after a few frames.
My camera generally takes a bit longer than 10 seconds to download - I have no idea if this is relevant. I did pause the sequence during a download and selected the finish frame option - the camera finished the download and then took another frame before the sequence paused.
I have a workaround and I am pleased about that - thanks again jmacon. It would be nicer if I didn't have to do this though.