I'm not sure if anyone else has this exact same problem but I've seen some similar ones in other post.

First off I have two accounts.
One was disabled back at launch because of a glitch, and it says "Unusable" on Account 1 (FFXIV1: Unusable Account).
Account 2 (FFXIV2: My Legacy account) is active, but it WILL NOT let me apply any codes.

When an attempt to enter the code is made this error appears:
"Services related to FINAL FANTASY XIV, including FINAL FANTASY XIV: A Realm Reborn Beta Version, cannot be registered with this Square Enix Account."

I noticed in the the Beta invite that it says that the beta key is for account 1 (FINAL FANTASY XIV1.
I've been wondering if I need a Beta key for Account 2 (FINAL FANTASY XIV2 then maybe it would let the account to be registered?

Beta is in less then 2 days, I seen lots of people got new codes issued to fix their registration issues. I never got such a code, or any response from any of my many attempts to contact SE other then "We need to escalate your case".

With luck someone out there had the same problem and found a fix.