Photomerge not including all photos - confused!

Hi,
I am using Photoshop CS5 12.0.3 to stitch together some panoramic photos using Photomerge but am encountering the following problem and would appreciate any advice.
I have 3 photos of a panoramic scene taken by the same camera with the same lens, focal length, ISO, shutter speed and aperture. The overlap between photo 1 and 2 is at least a third. The overlap between photo 2 and 3 is more like 50%. When I run photomerge (using the auto setting) the output image appears to only have photos 2 and 3 visible and merged nicely together. When I have a look at the layers photo 1 seems to be present but the output image doesn't include it. As an experiment I tried merging just photos 1 and 2 but that resulted in an image that just looked like photo 2.
This is confusing me - I have merged various other panoramic scenes with 2 to 5 photos taken on the same day with the same camera and set up with no problem at all so I think that rules out a lot of problems. I've tried this particular panorama from within Lightroom (edit in > merge to panorama...) and in Photoshop independently, both after working on other images and fresh after a reboot.
Can any of you shed some light on this please? It is driving me crazy. I am more than happy to provide the images if that helps (each is a 25MB Canon RAW file).
I hope you can help. Thanks in advance!
A

Have you tried other settings besides auto?
Also there is an optional plugin for cs5 that allows for manual alignment
of the photos during photomerge called photomerge ui, which places
an entry at the bottom of the photomerge dialog called interactive layout.
http://www.adobe.com/support/downloads/detail.jsp?ftpID=4688
more info (this is for elements since the cs5 help doesn't appear to have
anything on the interactive layout)
http://help.adobe.com/en_US/photoshopelements/using/WS27101fef35e777f9-2794c94411fdcce7142 -7ffd.html
MTSTUNER

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