I think you can only use one Kobo app at a time. I had the Australian Borders app and then had to download the Kobo app to get a book that I purchased from kobobooks.com that didn't have an ePub file. Ever since then I haven't been able to sync with the Borders app.
Personally I find it much better to download everything into ADE and use that. Then it doesn't matter where you buy your books: Kobobooks, Borders or where ever.
I don't think your Kobo is bricked - it's just that the two slightly different versions of the desktop app are interfering with each other.