Having the same problem…have you found a way to make this work yet? Just upgraded from x4 to x6 and cannot get the sync to work properly. I am getting the same error message.
I also sent an e-mail, explaining the same problem, and they proposed updating to x6.0.1. I do not have administrator rights, and the IT departement is having lunch all day…
You need to click on “EndNote Program Update…” under the “Help”. Close the EndNote X6 and continue with the updates then reopen your EndNote X6 library and sync.
This will hopefully solve your error, as it did for mine.