I am running Messenger Plus version 4.70.0.334 on top of Windows Live Messenger version 2008 (Build 8.5.1302.1018), all on Vista Business.

I have been using this combination for quite a while.  About 2 weeks ago the problem has started that no matter what application I am in, if I receive an IM, it will automatically pop up and my cursor focus goes right to typing in the reply section.  This is also true if I am in a single IM conversation and a second one pops up, my focus is moved to the new one.  This has become unbearable.  I have confirmed that Auto Accept Requests is not selected. 
I have completely uninstalled Plus and messenger, rebooted and reinstalled from scratch.  Still no luck.
What else could be causing this?  If I only have Live Messenger installed without Plus, I do not experience any issues.  BUT I want the features of Plus.  Any thoughts?

Check that you don't have "Always on Top" checked.

To verify this setting, just go to Tools and you should see "Always on top". A tick there means it is checked, no tick means the option is not in effect.

I confirmed, there is no tick next to Always on top.  That would have been way to easy

What about other addons? have you check through them?, addons for Windows could also have the option checked.

As an example, I use PowerMenu for windows so I can send applications to the series of icons next to the clock, this also has an "Always on Top" option in it. Therefore I would have to check that "Always on top" was not selected here as well.

I can not think of a single addon installed.  This computer has Windows, Office 07, Mcafee and our corporate vpn, nothing really past that.
If it were some other program causing the auto focus, would it not also happen to Windows Live Messenger without Plus installed?  Without Plus, i do not have the problem.