Problem for me appears to be sub-quality images, aggravated by high ISO's and/or long focal lengths.
The following allowed all the ISO 12800 sets to align roughly half or more of the images in a set:
Using 'Batch PreProcessing Script', Lights tab, 'Image Registration', set Noise Reduction from <Disabled> to 1.
The 2 out of 3 ISO 25600 sets still would not align. Tried numbers up to 10, still no luck.
These images were not nearly my best images. They all had some combination of deficiencies in focus, tracking, light clouds.
Further evidence of this:
My rig has a 90mm refractor at 630mm, and 200mm RC at 1624mm, both taking images at the same time.
All sets at 630mm PreProcessed perfectly. Only had the problems with the 1624mm sets. On other imaging nights with better quality images, similar 1624mm sets have all PreProcessed nicely.
Hope this helps.