I did a clean checkout of a repository then every day I have an hudson job that runs a script to backup the configuration. Part of the script is to add *.xml
This happened to me with netbeans where the GUI has "Commit" which is adding and committing as a single step. The solution was to use the command line, and call "svn commit -m "message", i.e. for some read the "add" step was already done when a file was copied.