This happened to both our new kobo touch devices that were bought at an affiliate (in our case Whitcoulls in New Zealand). The device was trying to connect to Whitcoulls, we were trying to sync using Kobobooks and we got the duplicate account error. We ended up changing the affiliate file on the device itself so that it didn't try to reference Whitcoulls. And no where in the documentation did it even mention that the device was set up to sync to Whitcoulls - it told us to use the kobo desktop, which we did.
When we have to do a factory reset we have to remember to change the file back again. I'm sure it is not what Whitcoulls intended but given that we already had a large library with kobobooks I wasn't about to swap to another store so too bad!
Not sure if this could be part of your problem, where did you buy the device.
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