This is the way I fixed My security Login problem after registering my token for FFXIV:CE.
After Registering my token the registration server went down for maintenance for about an 1-hr, and I was unable to login when it returned to normal. After multiple tries and password reset attempts I called SE and was told they cannot remove token. So I copied down one of the one time use passwords and tried to use it until i could login hoping that maybe the server side app. and my token had become de-synced due to the maintenance. Low and behold after 52-mins of waiting the token password was accepted and I was able to login and un-link it from account. I am writing this to anyone who may have the same problem I face and that maybe they will have an answer in this post.
1.) Write down 1 code from token.
2.) try same code until login.
3.) since code change ever 30-sec it is a shot in the dark as to how long the desync is out.
4.) can take multiple days to get timing right. (2-1/2 for me.)
Hope this post will help someone at some time in the future, since release has not started yet and population is still low.