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300 wow that's a lot.
Star detection of 2% , it depends on how many stars you have to work with, if you set it too sensitive it's picking up noise, I think it's unlikely to be the problem, that would probably just slow it down.
When I used to use a dslr I changed everything to TIF files first, it's possible for some reason it's not handling the RAW files properly. ( I work in FITS now with no probs) it would be worth a try, but it will make for a huge file.
You could also go back to a pre beta version, sometimes Beta has a few bugs.
For simplicity sake you could just do a simple average stack and darks with TIFs and see how that works.
I am unaware of any issues with stacking 300 images although 50 is probably about the most I've done.
Try those and get back to us.
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