Flag disappears after reading a message in Mail In Mail 9.0 (OS X El Capitan) I have set a rule that marks a message with a flag if it satisfies some conditions. 
When I receive a message which satisfies that condition, it is correctly marked with the flag, but when I read the message, the flag disappears and the message is automatically unmarked.
How can this be explained? I would like to always keep the flag, also after reading the message.
I reported this as a bug in 2006. It appears that Apple either doesn't use Mail or doesn't care about this feature.

You can get add-on software, such as Mailhub, to repair this feature.