An alternative is to use your current technique but only tick about 30 - 50 frames at a time. I will be a slow process but hopefully registax will be able to align the small amount of movement over that period of 30 - 50 frames. It will mean doing 20 - 30 runs but my feeling is you will get better images. You don't need a lot of frames to make one image of the moon. An extension of that idea is to go through the 30 - 50 frames and only leave ticked the good clear ones so that you end up with only 10 - 30 frames to stack.
Yep its a long slow process.
If you use Virual Dub make sure you save each section of avi under a different name so you don't loose the original