Hey,
I was affected by this as well and I found out when exactly this is happening. If you use the Popout-Chat function you will see the empty messages that OP talked about. Since an Iframe can hold the popout URL (for example https://www.twitch.tv/channelname/chat?darkpopout) chat as well you would see the empty messages. Using https://www.twitch.tv/embed/channelname/chat as documented here will fix the issue immediately - at least for embedded chats.
Regards
sanso
Edit: apparently thats not the case for everyone. At least I’m confident now, that its an issue with the chat client.