So is there any chance at all that this issue will be resolved?
After looking around several places...forums, facebook, etc it seems that there are many people in my position. The issu4e is the way that Square Enix handles their regionalisation.
Basically anyone that has a pre-existing NA account then tries to apply the code through the EU website with that account is ending up with a duplicate account and no game attached to the EU one (which is what the launcher is reading from in this case).

This is very firmly a Square Enix issue that should be addressed immediately, or comppensation given to those accounts that are caught out like this.