Hi Andrew!
This is the procedure I follow (rightly or wrongly) on Registax 6. It seems to work for me.
1. In Registax 6, select your video clip by clicking on the SELECT button in the top left corner of the screen (Photo 1).
2. Once the first frame of your clip appear on the view window, tick the ALIGN DATA box. My standard setting are per Photo 2.
3. At the bottom left hand side of the screen, select the best frame by going through the GO TO FRAME counter.
4. Click on the SET ALIGNMENT tab.
6. Click on the ALIGN tab. The alignment process can take some time depending on the size of your video.
6. Once the alignment is done, you get a series of yellow star-shaped patterns which show your the deviation from your set alignment points. If you use the GO TO FRAME counter to go to frame #2, you will see yellow circles and green lines going from each circle which tell you the alignment shift.
7. Using the GO TO FRAME counter, browse through your frames to select the one where only yellow circles appear and the green lines have disappeared.
8. One you have find that frame, click on the LIMIT tab (my standard settings as per photo 8)
9. Click on the STACK tab. This can take some time depending on the size of your video.
10. After stacking, the wavelet tab goes from grey to green, which means that you can click on it.
11. Apply wavelets as appropriate (photo #10 shows settings appropriate to the AVI I have processed).
If processing doesn't work in Registax, you can try Autostakkert 2 or AviStack 2.
I hope this helps. Let us know how you go.
Eric
PS I don't really have a technical knowledge of Registax. So I am not able to comment on the process itself as such.