After I installed VS.NET 2003 on a Windows XP Pro system
which had VS6 installed, whenever I start a VB project,
VB6 display a message box which says "Windows Installer -
Preparing to install". After a couple of seconds, that
box closes by itself then another displays with the
message "Please wait while Windows configures Visual
Studio .NET Enterprise Architect (2003) - English." That
displays for a while, a progress bar updates, then it
eventually closes and VB6 runs normally.

Apparently I can cancel either install message box and
VB6 runs fine. VS.NET does not display these messages.

Anybody know what's going on and how to stop this
annoying behavior?

I had a similar problem with mine. What I had to do was rename all the mso.dll on my system by searching for all of the occurances of that dll and then renaming to mso.dllold. Then repair my installation of VS.2003.

Hope this helps.