Trying a reinstall of the desktop can't hurt. You might use the standard uninstall routine in Windows (if on Windows) first and then install fresh from www.kobosetup.com
. Depending on your Internet connection and computer, it shouldn't take too long. At least then you can scratch that off as part of the problem.
I never log out of Kobo Desktop but, then, I also rarely use it so it isn't running on my computer except for one off uses.