I'm still having the same issue, too..
I purchased FFXIV via the SE website, not steam and the expansion through ShopTo. I activated the code I was sent by ShopTo and was sent a code by SE to use in the mogstation. The preorder activation site tells me I will be able to have early access and the items etc, and every time I go on it, it shows the mogstation code. But when I enter it into the mogstation, it keeps telling me it's invalid. I made sure it's all caps, I tried typing it and pasting it in, no luck :/