That probably explains a lot. Maybe I was cleaning up and figured there was no need to keep the “2” in the name and that somehow made it look like two different products that install to the same folder.
Ok, that makes a ton more sense. So it is an upgrade issue that causes all the problems 
That is something I can debug fairly easily.
I can see that this part was removed from the new MSI because the wixl tool does not support the condition required to disable them. I will see if I can tweak it to add those conditions back in.
Alternative could be to install with something like this (tested):
msiexec /i file.msi FORSERVICE=true ADDLOCAL=ALL REMOVE=DuplicatiDesktopShortCutFeature,DuplicatiProgramMenuShortCutFeature,DuplicatiStartupShortCutFeature