Mail has mystery flags?

I use rules to filter incoming messages into folders and mark them with flags for review. Before upgrading to Mavericks, once I read an email the quantity badge decreased. If all messages were read the quantity badge disappeared. Messages remained in the Flagged box until I "Un-Flagged" them. Now my five flagged categories each show badges with various quantities, however I have "un-flagged all messages and all folder have no messages in them. Any Ideas?

Friends I believe I've found the answer. At least it worked for me. I went into each mail folder and just looked at the list of messages. As I looked in each folder the quantity of flagged messages reduced. I looked in the folders that each specific flag was associated with. I.E. I renamed the red flag as Payments Due. So I looked into the folder where I would store those messages and it adjusted the phantom quantities. Let me know if this solves the issue for you.  Cheers!

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