It's likely to be a plugin not finishing it's job properly IMO. Although if you can close Messenger anyway (
not via Task Manager
)... well, disable plugins and see what happens then
As for MessengerDiscovery, that uninstaller bug (clearing out startup items) has been there since version 2. It wasn't until I upgraded Spybot one time and got the Resident that I knew it was MD doing it. MD also doesn't reset Messenger's connection settings, causing further problems. Not to mention it's buggy, can be unstable, and rather barren, feature-wise...