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Thank you for your patience and sorry for the lack of info. I believe that I got it now. You're right that the directories in question are empty. When performing an action on a version controlled directory subversion depends upon those empty directories in the .svn folder to be there or the actions, be it update, commit, whatever, will fail.
Now, I didn't realize that the list files will exclude empty directories. I don't understand the necessity of that but that is besides the point.
After tooling around with the issue some more I realized that what is happening is that when the option to delete empty folders is checked it in fact does not honor exclusions. I can work around these issues now that I understand the problem.
Thank you for your assistance.
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