Might be an idea to change this to Ray's suggestion box.
Would it be possible to take one short additional exposure prior to each imaging run, short enough for a reasonable number of stars to be captured depending on the filter being used.
What I believe is happening from looking at the FTS header data, is that some control software is checking an image taken to ensure that the scope is reasonably on target, and then repositioning if not. Having never used any software for telescope control, I may well be incorrect on this. If I'm correct then this short exposure will ensure that all subsequent images are aligned.
Ray