A possible clue to follow...

My message indicator has been showing two unread messages since the update.  Upon doing a bit of investigation in the SQL database ow_mailbox_conversation, I found two entries which were both encoded as not having been read by interlocutor or by all or having been deleted.  I know for a fact I read and deleted both of these conversations.  The interesting fact here is that both conversations were with a member of the site who have deleted their profile.  Perhaps this might help explain what is going on.

When I manually edited the SQL database on these two instances to show the correct condition, my message indicator reset to 0. 

After digging deep into the database, I believe I found the issue of why this is occurring.

This is what I did and everything for me is back to normal.

1.) Go to your database -> phpMyAdmin

2.) locate and select your database for your oxwall site (if you have more than 1 database, make sure you select the one that corresponds to your oxwall site)

3.) Scroll down until you see this table -> _mailbox_conversation (you will probably have a prefix in front of mailbox [e.g., hp_mailbox_conversation])

4.) Here you see all the conversation ids between users -> There are 2 things you need to look for.

They include:

1.) Subject

2.) Read

Under the "Subject" -> locate any item that says mailbox_chat_conversation

follow the path to the right from the Subject until you are under the "Read" column

If it states "1" under the Read -> Delete the entry

"2" and "3" you can leave as 2 stands for the person who received the message has read it - and 3 stands for both parties have read it.  But 1 stands for only the sender of the message has read it - therefore, any item listed in that table with 1 and corresponds to the mailbox_chat_conversation under the subject area needs to be deleted.

This will take some of you time if you have a large user base.  But this works and is a temporary fix until the devs figure out why this occurred in the first place and release an update.

Thought I'd share how I got this to work on my end - so far no drawbacks and everything is working smoothly and FINALLY no more unread messages appearing...

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So, to help out the devs of this plugin, the conflict lies with the mailbox_chat_conversation, (e.g., the IM part).  Might be something you want to report to the devs about Ross as I'm unsure if the devs even look at the forums here...

Quote from Robert Rodrigues Hybrid82's quick solution fixed the issue for me.