OK, I think I found out what was going on. Have a look at http://www.southportway.com/portals/12/southport-tour/virtualtour.html
and see you think it looks better.
We had adjusted the "Input Field of View" by changing the Vertical to 180 to get the Nadir patch to show up. Once we reverted this it looked OK. I do have a few specific questions though:
1) Is there anyone to "batch" setting have APT revert these Input Field of View values back to the default calculated value?
2) When I edit an image and use the "Spot Healing" brush in PhotoShop to remove the tripod, APT can't calculate the Vertical Offset in the Input Filed of View and I get red exclamation marks beside it.
3) Is there any way to get the Nadir patch to show without changing the vertical field of view to 180? We are coming from another software package that would allow to to use a patch to fill the area we didn't shoot so you end up with full panos. We are adding this Nadir patch under Project Properties > Extras > Logo > Nadir Logo
Thanks so much for all the help. I really do appreciate it.