I kind of had the same problems . Read and narrowed it down to this . 1. Crop all the stacks before trying to merge the panels. 2. If some panels won't merge it is due to lens distortion . I can do 3 to 5 panels with very little problem but anything over that and it just won't merge due to distortion. One solution is to make a synthetic star field according to a David Ault tutorial . Looks like you are using a small refractor like me , 80mm.
http://trappedphotons.com/blog/?p=994#comment-394
Hope this helps.
Dennis