Photoshop :: Photomerge Segments Panorama And Isn't Stitching Properly

I decided to take a panorama of the beach I was on, and as a general the photo's came out well and all have around 20% overlap, however when I put the photos into Photomerge in Photoshop CC or CS6 it results in this:
 
As you can see part of the image decides to float above another part and there's even one below the lower segment. The panorama itself is 22 images, but I only used eight to try and find out if the problem was the number of images, it appears it isn't. I've tried both the "auto" and "perspective" options under the Photomerge dialogue, neither works. It should be noted that before it "blends the images", under the layers section, all of the images do line up.
 
I'm using the images in their RAW format (.NEF), although I did try in the .jpeg as well, neither worked.I'm running Photoshop under a VM as I'm running Ubuntu, although I did try on my Windows 8 laptop as well, again neither had a good result.