Photomerge and Auto Align/Blend issues!!! HELP!

I have a lot of photos that I need to create panoramas of, and when I use Photomerge all of the photos that I want to create a panorama of show up on the same image, but are stacked one on top of the other. Not linked or mergedin any way. They all have vector masks, but nothing covered up. When I try to use the Auto Align and Auto Blend modes for a panorama, an error box shows up saying that I don't have enough coverage area of 40%, but I certainly do. They images are very similar, and taken by standing and moving 360 degrees. I don't understand why Photoshop doesn't like these images? But I have to make about 100 panoramas, so any and all help and insight would be greatly appreciated!!!

What OS are you running? 32 bit or 64 bit? How big are your source images and how many do you have for a given pano?
I just did a 360 degree pano that ended up 25689 x 1850 pixels (after cropping) from 17 raw Canon 40D images, all handheld while standing in different spots around the Clingman's Dome observation tower in the Great Smoky Mountains National Park. Photoshop CS5 standard 64 bit on Windows 7 x64 with 8 GB RAM didn't have any problem at all with it, though it took about 10 minutes or so to finish. The result came out astoundingly good, even though the slight changes in perspective should have been challenging.
http://Noel.ProDigitalSoftware.com/temp/ViewFromClingmansDome_NPS.jpg
If you don't mind my asking, what do you do with hundreds of panoramas? It's an difficult image format to find uses for to say the least.
-Noel

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