although i can see in the fits header that you did have linear fit rejection turned on, there seems to be some hot/warm pixels still hanging around in the integrated image. from looking at just one sub it's hard to tell what the sum of all your other subs is going to look like... but generally speaking when you have subs with slightly misshapen stars, integrating them with good rejection parameters will tend to fix the star shapes a little bit as long as there's no consistent error in the star shapes in every sub. but in your integrated images the are pretty messy.
also what if you blink all of your registered frames and zoom in on some stars while the animation is running? is everything jumping around or do the images seem well aligned?
i wouldn't say it's common, but if there are a lot of hot pixels in your subs then sometimes StarAlignment will be overwhelmed by those hot pixels and end up registering all of the frames with no offsets, since the hot pixels are always in the same place in each image. the raw sub you posted looks fine, but i wonder what a calibrated sub looks like.
rob
