Thanks for the help, GRiker. I think I figured out that even though I thought I was editing the copy of the file that was in the configuration directory under application data I think I was actually editing the version in the main Calibre program files directory. Which of course would mean that the configuration directory copy would override the file I was editing. <headdesk>
I am curious, are there any custom columns types that it won't work with? Or, so long as there's data in the field, it will work with any column type?