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without seeing screenshots of a single frame and the result its a guessing game.
initial thought is its not aligning properly, maybe some frames had cloud cover throwing things off.
were you tracking? are you expecting movement of the disc in the video?
I would try using PIPP to dump the video to frames ordered by quality so you can look at the best/worst frames. you could also then retry registax with the best five frames (no need to use limit in R6 of course). if you are recording full disc use PIPP to center the sun and export best N frames to pics or AVI then run that in R6.
basically try reducing data to a couple of good frames to test your r6 process before expanding to more data.
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