Question

I registered the product on the Clarivate EndNote site during the installation.
Despite having done that, when I open EndNote X9 it shows my copy as unregistered and keeps giving me a blank registration pop up window.

Solution

That can sometimes be either a connection issue or a display issue.
Another route you can try:

1. From EndNote X9, go into Preferences>Sync
2. Click Enable Sync
   Here you should be able to either sign up for a new account or activate the X9 entitlement for an existing account. This can also sometimes bypass the issues from trying to use Tools>Sync to trigger the entitlement.

I have tried all of the above in turn, what now?

Try, in EndNote, opting to register a new account, then put in the same email address as your existing account. That can stop the pop-up box and update the subscription details on the Clarivate EndNote website.