This has been an issue for many years, and still an active problem in version 
38.4.0.
One cause is the use of Message Filters. When a filter moves a message out of 
the inbox to a local folder, the original inbox (which has no more unread 
messages), is still displayed blue and the unread tray icon is active. When the 
moved message is read in the local folder, the unread tray icon is not removed. 
Going to the original inbox folder resolves the unread indication.
I think when moving a message from any folder, it should be checked that it is 
the last unread message in that folder. In that case the unread indication 
should be removed from that folder (and put on the folder that the unread 
message is moved to).

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https://bugs.launchpad.net/bugs/291827

Title:
  New mail icon doesn't always hide

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