Can you try this fix from the common issues section in Fluxer HQ?
Problem: I have a stuck mention or unread indicator.
There are some known issues with mentions and unread indicators getting stuck in certain circumstances. We're working on finding a reliable way to reproduce the bug. In the meantime, you can resolve this by marking a message in the chat as unread, then marking the chat as read again. On desktop, you can do this quickly by Alt-clicking a message and then pressing Escape.
Other times, simply reloading the client will fix it.
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Comment by ternera