I don't think it's Messenger Plus! (it's Messenger Plus! or MsgPlus, not MSN Plus!) that interferes with email notifications. I have been receiving email notifications a lot (mostly junk/spam
) and I actually want to take it out (it's annoying and really loud when you turn your speakers full-blast for watching movies).
If the default conversation in grouping conversations was not the one that you received a message from, Messenger will automatically switch that active conversation to the default and highlight it. I don't know what the problem is with your Messenger.