Hi Erin,
I have no experience with imaging with SCTs, but it does look like optical misalignment, often sagging focuser is to be blamed for that.
However, stars not matching perfectly across the image may be also caused by field rotation between subs due to inaccurate polar alignment. When stacking images, I always correct for field rotation and have found this method gives very good results. I know that Nebulosity and PixInsight can correct for field rotation, but have not used DeepSkyStacker and Registax only a few times ages ago, so I cannot comment of their capability to correct for field rotation.
Good luck and let perseverance and patience be your best friends
