Re: problem with stitching. nadir in the middle of photo
Sounds like your pano is now centered on the vertex, not the nadir. Just use the centerpoint tool, click on a point to the left (or right) of your pano that looks like its on the horizon or where the horizon should be. Then use the 90 degreee rotation tool. You may have to do a 180 rotation if you pick the wrong 90 degree tool (one goes clockwise, the other counterclockwise)
If the nadir is missing, look for the photos or panos that are unlinked.