I see a notification for message from discord but it never shows up in game.  I am wondering if discord can yank it off the queue before it shows up in game chat.

I think it almost always shows up in battlemetrics but I think i saw one even it missed.  

If you are referring to: https://umod.org/community/rust/24988-not-showing-chat-messages-sometimes

That would be a client bug I believe with Rust.