It could be a file permissions problem. You can use Disk Utilities to fix permissions. You can also try to save it in a different location. Sometime I find Acrobat Pro 9 under 10.5.x thinks I'm root, when the OS knows that I am not and it tries to have me save in root's Document Folder or Desktop..
I think you may be right. I tried saving in a different location and that didn't work. Then I discovered permission problems with some files. I'm adding file by file and saving after each one to see if that works.