Jules, if you comb through the Process Console list after you have Registered these subs, you my find several subs that have a large offset and or rotation.
A note on the Reference image used for StarAlignment, if you use (View) for the Reference image, (you have opened a sub) and leave this sub file open it will be used as the Reference image for Integration.
After I stack with Integration and have Pixel Rejection set to Winsorized Sigma clipping, I will again look at the Process Console Rejection list for any subs that have large rejection numbers.
I hope this will help.
Cleon