Patchou, sorry but looks like you're wrong on this
I have exported my prefs and contacts stats of my main account. (Maybe exporting prefs was not necessary but I did it because I saw a "ContactWatchTime" value in registry under Preferences root of my main account and I thought it may be related with Contact List Clean Up). Then I signed in my test account, then added one contact who I had a chat 12 hours ago. I looked at Contact List Clean Up window but it was showing the last chat as "+3 months" like expected. Then I imported that preferences pack, which includes that contact's statistic also, then re-open Contact List Clean Up, voila, it showed the last chat as "12 hours".
shadowsx, as Patchou said, you have to import preferences, particularly "Contacts' Settings and Statistics" to your new Windows Live Account. Then if you import your previous contact list, or any one who was in your previous contact list, then Messenger Plus! will show the real last chat and last online time with them.