Do I feel like a dork or what?
I found out I was half way through a search in regedit and decided to continue searching for these settings. A minute later I had found the reg keys and made the changes.
So new question:
Will "DESKTOPSHORTCUT", "PROGRAMSGROUP" [EDIT] and "ProgramsShortcutPath" [/EDIT] in "HKLM\SOFTWARE\Paint.NET" affect the installation when it is started by Paint.NET itself?
/M