Messages fail to register as read / unread badge comes back for read messages

For a couple months now, I have been faced with an incessant issue across two windows clients, an android client, and a web client that I use, where someone will send a message, and I will read it, and the "new" unread notification fails to go away, or, if it does go away initially, it will often come back! 

Clicking on the client, back and forth between the client, or navigating channels within the client all do not update the last message. I must either manually mark as read, or send another message in that channel. 

This does not happen for all messages, and I cannot figure out when exactly it does happen, but it is very often. This did not used to happen at all. 

I don't know why this isn't working. If the client is interacted with while the message is shown, that message should be permanently marked as read.