Shoutbox

First of all we are not Microsoft! It sounds like a bad install of Windows Live Messenger, so try uninstalling Messenger Plus! then Windows Live Messenger. Install WLM by its self and see if the problems continue. If not, install Messenger Plus! again and see if it all still works.

It is very unlikely these issues are being caused by Plus!

Scripts have the same powers as EXE files when it comes to security, but all scripts on the official database are moderated. Even if you had downloaded a script, it is again very unlikely to contain any malicious code.

You mention you gave nod32 and Malware Bytes Anti-Malware. I'm not sure, but your System Restores may have rolled back your virus definitions leaving you vulnerable to certain types of attack. If things start happening again, open Windows Task Manager and check the running processes for anything you don't recognize. It is most likely you have a trojan running on your PC allowing a remote user to take control.