I was reading your post more carefully and if I understand this correctly he gets the filed messages during the Activation but they are not in the specified folders, just the main messages folder on the BB? Then he has to file them?
That's different. I don't usually have people that use sub folders so much so I don't usually troubleshoot mail redirection before activation.
And you have selected the folders prior to the activation as well?
What is the exact process that you are following?