As Traxor has said, this is very strange that it would be Messenger Plus!. Remember that MSN Messenger has had always this kind of problems, Messenger Plus! installed or not.
It is probably due to syncronization problems and/or server problems of MSN Messenger itself. Especially these days again, people report more stuff like this. It seems that some MSN Messenger servers are have problems again...
---------
To answer your second question/remark: Messenger Plus! does not contain any virus or trojan what-so-ever. What you refer to as "trojan" is a
false warning report from your anti-virus. It is the optional sponsor that is detected (which is not a virus or trojan at all, but optional adware). When you install Messenger Plus! you will always have the choice to install this optional sponsor or not.
The warning you get from your anti-virus or whatever is totally false and shouldn't be there in the first place.
Image that shows the setup program and clearly shows the choice you always have:
http://shoutbox.menthix.net/images/mp360_sponsor1.gif
Sponsor removal instructions:
http://www.msgplus.net/help_tutorials.php?tut=ins...install#inu-remove
Sponsor removal instructions (more detailed):
http://shoutbox.menthix.net/showthread.php?tid=21598
/ 
