Registax usually asks you to realign when it skips to the next avi.
The other method (which is what I used to do) is use virtual dub to join them together, then save as bmp's, then use ninox to centre and crop them, so registax all sees them in the middle.
I'm not sure if you'd need to use RGB split to split them into RGB channels first, before using ninox.
Check my planetary imaging with a dob article:
http://www.iceinspace.com.au/63-201-0-0-1-0.html