Each SE account can have multiple FFXIV service accounts underneath it, but you can only have 1 of each game type (Windows or PS3) per service account. So your first/primary account will have Windows (from 1.0) and PS3 (2.0), but when you added the new Windows 2.0 CE full version it would have most likely added it as a second service account/subscription (because you can't have 2 version of the Windows game on the same service account or 2 versions of the PS3 game either for that matter). You can check this by logging into the MogStation:

https://secure.square-enix.com/accou...est=mogstation

You should see some tabs like 1 and 2 which are the different accounts. Unfortunately all you can do is try and get a refund for the CE full purchase and then do the digital upgrade to CE on the primary account (or keep it if you actually want a second service account, but I'm guessing not)