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Are you sure that you're using the files that were output by the StarAlignment process? I just helped someone on the PI Forum with the same issue. It turned out that the registered files were going to a different folder from the one he expected.
I've never heard of StarAlignment failing to register images without displaying error messages. It would be worth checking through the process console log carefully. Another thing you could try is opening a few of the files and applying StarAlignment to them as views and watch what happens.
Cheers,
Rick.
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