Issues with Panarama's in Adobe PShop CS4 extended

Hi folks... probably an easy answer here but it has evaded me so far so hopefully someone here might know what is up. 
I shoot up to 6 sometimes 7 (vetically shot) images for a pano in Raw.  I shoot vertically so I don't loose as  much sky or foreground.  I then pull the shots in using Bridge.  I open Photoshop CS4 extended, click on the pano menu item, select my images, choose the top left side choice and click on all three fixes bottom right under the window... and press OK.  Once PShop is finished the shot is set up as a portrait style with some images put together and some not.  I could have three beautifully put together up top then just below it only one shot and below that, the balance put together.
Why would this be in a portrait format when it is wider than deep?
Why in pieces still?
Is there a limit to the shots needed to be used?
Thanks  Kate

Chances are you simply haven't overlapped the shots enough for it to find the commonality between the shots - or something changed between shots.  I have had very good luck with Photoshop's Photomerge function if I overlap shots by about 1/3 each.
Is there water in your shots (e.g., with waves on the surface)?  That changes from second to second at the detailed level.
Could you make small versions of the shots that don't seem to want to stitch together and post them here?  I might be able to better help nail down the reason it's not stitching them after looking at them.
-Noel

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