When moving over from using Gmail via MS Outlook to OS X a little know error sometimes occurs with labels and folders.
If Apple Mail reports "Mailbox Does Not exist", or Thunderbird gives "[Nonexistent] Unknown Mailbox" then all you need to do is rename your labels.
Folders created in Outlook became labels with the name Inbox/FolderName. But OS X Mail and Thunderbird both look for INBOX/FolderName. Simply edit your labels to change the case and all will work fine.