Are you taking the T+B shots on the 6th click stop position ?

As Smooth says :

Hmm let me think on this issue.

Using a Sigma 8... I click around with 4 images and stop at the 4th click stop and then rotate the camera up to the zenith.. take a shot... then rotate down and take the down nadir image.  I am done

Take all 6 [4+2}  images into Panoweaver ..the software is able to bring all images in together.. properly.

Should be same to 6 +2

Most likely the camera has been set to rotate images automatically and when shooting the Zenith and Nadir the camera is getting confused with the orientation as it relies on gravity and in the Zenith and Nadir shooting position this would be a 50/50 bet. Simply turn of any rotation values set within the camera menus.

Just to be 100% clear all images should be shot in the same portrait orientation with the Zenith and Nadir shot on the sixth and final shot position. 

Regards, Smooth

I agree with Smooth,  I too have noticed that the camera internal sensors are trying to understand which side of the image is top  when pointing the camera down or Up.

For Canon SLR's like the 20d and 5d,  it is the menu item called 'Auto Image Rotation'.   During playback display on the LCD the portrait image will dispay the image top in the UP position. 

I also think there is a Auto Image Rotation flag recorded in the images EXIF header area.  Because when I take nadir/ zenith images into Photoshop PSCS3 attempts to display them on the monitor in the direction IT thinks is image top UP.  Which is very annoying.  I can not tell if the portrait image is really taken properly top up... or is PShop just displaying a landscape image in the portrait direction "auto rotation"

Best turn OFF the Auto Image Rotation menu item in the camera.

If the zenith and nadar are plain ceilings and floors or sky and grass it is often easier to patch the holes in Photoshop.  You can also put your logo over the tripod which further reminds your guest of  your company name or brand.  There is usually not much information in the zenith or nadar area to begin with so even limiting the tilt up and down is not taking away to much from the viewer.

Good Luck
TTurner

It seems to me from my limited experience of shooting panoramas that it would be prudent to go through your respective camera settings and turn off everything that is auto!

I have had issues linked to various 'auto' settings on my camera and have now turned off all my 'auto' settings.

Regards,
Steve