I manually merge mosaics in photoshop, I never tried to use automatic software.
If you put the original files on dropbox while you are waiting, we can download them and take a look/have a go.
Dropbox gives you 2GB of space and is completely free. I'd love to take a crack at your data!
If you use the link below for dropbox, you get 2.5GB, we both get extra space
http://db.tt/f05Ft1e6
That second autopano shot is an improvement, but 'hot cross' at the 4 panel boundaries is still present.