The only thing I can think of is if you had other characters and it was mixing them up, or if you did the whole process too quickly (it can take anywhere from 1 hour, to 6 hours, to 12 hours or even a week to update the lodestone information including your character's FC, depending on server congestion). For example, after Dawntrail, many characters took over a week to update, while now it's less than a day. It updates the lodestone more when server activity is lower, so doing the whole process slow the way SE likes it might help.