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I found the same thing with ppmcentre - it crops the moon out no matter what settings I used.
I emailed Anthony this morning to see if he can help.
I've stopped using a large alignment box in registax - I now use 128 and put it on an area of interest (ie: a nice feature/moon shadow, GRS, etc). I actually think Jupiter is big enough to do a multi-point alignment on. I think given its size, there are bound to be frames where one half of the planet is sharp and the other half blurry.
I'm planning to try that on this processing run if the images are of good enough quality. Adds a lot more time to each processing run, that's the only downside.
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