As far as I am aware, the Packages folder holds installers not installed programs. I would suggest redownloading the
Kobo Desktop App for Windows from Kobo's site and re-installing it. You might also want to try uninstalling the KDA if it shows up as an installed application since it sounds as if something went severely wrong with your install.
On my system, OBOK does not point at the folder where the downloads are stored but at the Kobo Desktop Edition folder and the plugin looks for the kepub directory inside that folder.