Which version of registax are you using? Procedures may be a little different between versions.
I'm currently using R6, so without knowing any specifics of what version you have or what your processing workflow is, I'll detail mine in case it shows something you've missed.
1. Load the video.
2. Step through frame by frame to find a sharp one, then create multiple alignment alignment points on that frame.
3. Align.
4. Limit the frames to the quality level you want, or the best # you want. I am only just starting to try limiting to the best #.
5.If you limited by quality, then on the stack page open the stackgraph and slide the slider on the top graph to the left until the number of frames to be stacked (down the bottom of the page) is about 100 (you can choose what you like).
6. Stack them, and save the file as a BMP or TIF with a suffix like Sun1 or Jupiter1, etc.
7. On the wavelet page play around with the wavelet settings till you find a combination that gives you a nice sharp image (without artifacts). Save that wavelet setting if you haven't already, so you can quickly get there next time.
8. Press Do All, and save the file as a BMP or TIF. I add a different suffix like say Sun1w so its different to the unsharpened file.
The reason you limit to quality, then later use the stackgraph is that with multiple alignment points, you have more good quality
parts of images to choose from. If you limit on the frames to start with say to the best 100, you may be throwing out some parts of other images that may be better, just because most of the frame is worse. Likewise, if you don't limit the frames you stack, you're just stacking rubbish and diluting the good frames.
BTW, in statistics about 30 is generally considered the lowest reasonable sample size for stats like RMS and SD to reasonably reflect an infinite population, so I use that as a guide to a minimum desirable stack size. Its better to stack more, but there's no point in stacking rubbish (So I have been known to stack as little as 2 frames if that's all I've got that's any good!)
I hope this helps.
Al.