What is happening is there is an installed VS.NET component referenced in your system registry which itself references xml configuration files which may or may not exist on your system - even if the installation of that component has been successful. When one of these xml files is not found, Windows Installer kicks in and tries to "fix" things. Uh thanks MS. Of course VB6 itself does not care about any of these xml files.
Fortunately, creating zero byte files with the paths and names it is expecting should make the problem go away. To find the names of the missing files, open your Event Viewer (just type "Event Viewer" in the Windows search bar or go to Control Panel\System and Security\Administrative Tools > Event Viewer) and navigate to Windows Logs > Application. You should see a pair of yellow triangle "Warning" icons attributed to Windows Installer near the top of the list - the missing file will be shown in the first (lower) of the two events.
Create that missing file and run VB6 again. Refresh the Event Viewer and look for the next missing file, create it, etc. until the error no longer appears.
Note that due to folder security settings, it is probably easiest to create each file in a location which you have full access to (e.g. your Desktop) and then copy the new file into the destination folder.
The missing file names themselves may vary, but this is what I had to create to solve the error with VS 2010:
- C:\Windows\Microsoft.NET\Framework\v4.0.30319\WPF\System.Windows.xml
- C:\Windows\Microsoft.NET\Framework\v4.0.30319\Microsoft.VisualBasic.Vsa.xml
- C:\Windows\Microsoft.NET\Framework\v3.5\Microsoft.Build.Tasks.v3.5.xml
- C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\v3.0\en\Microsoft.ManagementConsole.xml
- C:\Windows\Microsoft.NET\Framework\v2.0.50727\en\System.Configuration.Install.xml
- C:\Windows\Microsoft.NET\Framework\v4.0.30319\RedistList\VSList.xml
Hope this is helpful.