The first password is to unlock the boot drive so that the computer can boot. That part isn't considered as part of the startup time.
The progress bar is the boot process itself.
The second time you type the password is at the login screen.
That is not the default setup. Normally your login password and FV password are the same and you just enter the PW once and it goes right to the desktop. Sounds like you have yours setup with two non-matching passwords. You can change that if you want to have one password, which is what I have and is the default.
Then using FV is just like a normal login.
They are the same password. It started when I did a new install of Yosemite. I must have turn something on that I didnt intend to do.
Did a little research and apparently this is a known bug - http://www.macissues.com/2014/10/27/filevault-bug-makes-yosemite-pause-or-hang-at-login/
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