I would wait maybe 24-48hrs more, and then check back after fully logging out and logging back into the site, and trying again. If not, may need to check with customer support. Did you happen to have ANY free days given to you by squeenix or FFXIV's system? As those do not count in your 90 days if you received free time from Squeenix, and may need to minus the days off to adjust for how many days left you need to make for full 90 days.

Some of the newer servers like midgardsormr give 15 days extra added time to the account after you hit level 30 with your first job in the new server with the XP bonuses. Therefore, would need to -15 days to get the true total of the subscription time period left to make the 90 days.