I just had the same problem. This is is what I did.
1) uninstall the Kobo desktop software
2) plug in your reader, choose "manage"
3) Look at My Computer in Windows (not sure where the various drives show up in MAC)
4) Open the Kobo Drive from there.
5) Click on desktop installers.
6) Choose windows or mac and install from there.
This may be the long way around--you could try uninstalling and then reinstalling from
http://www.kobobooks.com/desktop
BTW, what OS are you using. I am on Windows 7 64 bit.