Hmm, I did see that thread but I’d missed your posts-- does seem like you’re encountering the same issues I am. Poking around the chat window in Chrome’s DevTools actually revealed something fairly interesting. Looking at the open websockets it seems like the chat window opens two connections to the IRC server: one for general chat traffic and one that specifically listens for inbound whispers. Any whispers sent to my account were still being received by both sockets, so I went ahead and threw together a quick extension to display the messages inline with chat manually.
Of course, after going through that exercise, today my whispers started working again same as they always have. Not sure exactly what changed; I noticed BTTV needed some new permissions as well so seems possible that there were some updates to the chat system?