It's a feature....er bug. It's known. But it Cryptic devs can't fix it. It's up to the Account server programmers to fix it. And it's not that much of an issue now. There is a button on the game menu to return to the character select window directly. No need to log out to switch characters any more.
Yeah, I noticed that when I got logged out for any reason, the game saved my Cryptic handle (which, since I've played PWE games for a long while....the last time I used my Cryptic handle was when I logged into STO pre-account merge. That wasn't an exceptionally long time at all.).