Hi Chris,
The default StarAlignment settings generally work for me and I've never had to tweak the basic alignment parameters to get a good alignment. I have heard of cases where StarAlignment was confused by hot pixels, so I guess that's a possibility.
Can you upload your reference and a small number of subs to Dropbox or somewhere similar? I'd be happy to have a play and see if I can reproduce the problem and then look for a way to correct it. Also happy to dig through the process console log and see if there are any hints in there.
I'll send you a PM...
Cheers,
Rick.
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