If you don`t want to make control points manually (I usually do, as I said) you can also try to make them automatically in parts. Go to the Image tab, select only part of the images (like those correspondent to one only horizontal line or those that were disconnected) and with them selected press the button to create the control points.

You can also do that after the global point detection step. I also don't have good experience with optimization made automatically. I usually do a first step to one horizontal, in three steps, y,p,r / y,p,r,v / Eveything without translation.

Anyway, I also know that many people do spherical in different ways. It is really usual necessary to try many alternatives to find the best way for you and in the middle try to understand the details. If you search for "recipe" or other words in the list history you will find many ways to do the same thing. Here is an example.

For a spherical it is also very important that you have used a panoramic tripod head. Without it you will have much more trouble to solve.

Cheers,

Carlos E G Carvalho (Cartola)
http://cartola.org/360
http://panoforum.com.br/
http://gnugraf.org/