I think I managed to fix this by optimizing all my luascripts. I have a ton of them that are connected to onTextMessage and they were all connecting over and over again with auto(100) or so because I had other functionality in the scripts. When I re-wrote everything and made it only connect once per function when I started the script it started working much more reliably. So you can mark this as a non-issue.
It appears that since the last update using: connect("g_game", "onTalkMessage", checkMessage) is much less reliable. I tested it with multiple clients all on the same screen, and it often misses messages (either in default chat, or monsterspeak both are sometimes missed) I use this for a variety of things so if this could be fixed to catch everything again it would be super-awesome. Thanks!