If you have a converted profile and you see an incorrect notification in the navigation bar, please read further.
If you have an unconverted profile on the same account as your converted profile, switch to the unconverted profile and access your 'old' inbox that way.
In your inbox look for the same amount of (read) messages you see an indication of. For example, if the navigation bar incorrectly shows 2 notifications and you have no new messages, you'll want to select 2 messages in your old inbox. Mark the (read) message(s) as unread. Refresh the page and mark them as read again. This will remove the notification(s) from your navigation bar.
If you do not have any unconverted profiles on the account this is happening with, please post here.
Yuku is looking for the exact steps to reproduce this issue. In order to do this, they'd appreciate an answer to the following questions:
1) Does it happen each time after you receive and read a message? yes/no
2) Do you access your inbox via the navigation button while on a board, or by clicking on the message indicator, or by clicking on your profile and accessing your inbox from there?
3) Does it happen to all messages? (messages you reply to and messages you don't reply to)
4) Do you always delete your messages after replying to them or do you leave them in your inbox?
5) Do you manually mark your messages as read or do you just read them without ever touching the mark as read/unread?
6) Do you generally receive messages from the same people or a variety of people?
7) If possible can you check with the sender of the message(s) and ask how they were sent? (e.g. via the interact menu on a board, by manually typing your name in the to field, by replying to a message you sent first, by going to your profile page and clicking write me)
If you have questions, let me know. If the notification annoys you, they can manually clear it for you.