I appreciate you said you bought the pack from Steam, but were you already playing the game before you bought the pack? (possibly bought it just to get it all on Steam?)

I only ask because it just seemed strange that you would get to level 50 before trying to register the expansion which suggests you already had an account/levelled up already. Apologies if I'm wrong.

Sadly the expansion code that comes from Steam will only work if your base game also came from Steam (the code). The game files for both Steam and non-Steam versions are exactly the same, just where you get the code you register your account with flags it as Steam or non-Steam.

That's assuming Steam even issues two codes, from my understanding the non-Steam bundle is a single code that registers the game and expansion all at once (which can't be used to upgrade an existing account either).

Sorry I realise there's a lot of assumptions in my post here so I apologise for any that are wrong, but if you are playing/registered the account with the ARR code that you got from Steam as part of the bundle you need to talk to Square Enix/Steam to tell them the second code isn't working, but if it's weeks later they might not want to know any more.