Please note that Recovery HD must be present on your computer's startup volume to use FileVault 2 (not an external Recovery HD).
When you've completed the process of turning on FileVault, you will be prompted to restart your Mac. After restarting, you will notice the login screen appears very quickly, then an Apple logo with spinning gear appears after typing in your password. With FileVault 2 enabled, you are now logging in at EFI which unlocks the drive and begins the normal OS X Lion start up process.
The user account that unlocked the drive will be logged into their own account after start up completes, without needing to log in again.
If you want to make the Mac available to a user that does not have unlock capabilities, log in, then when you see your own desktop, choose "Log Out (user name)" from the Apple () menu. Also, you can unlock the disk, then choose the other user's name from the Fast User Switch (appears as the currently-logged in user's name) menubar item in the upper-right part of the screen.
FileVault should finish the initial encryption of your entire hard disk within a few hours. This happens in the background, and won't interrupt normal usage of your computer.
... just part of the in-depth article
https://support.apple.com/kb/HT4790
I think the article misleads people with "entire hard drive" as it would only apply to the Mac Standard HFS and probably only where the system resides. Not sure what happens with multiple partitions. Is not going to touch Windows partitions.
Your issue would seem to be an issue with FileVault2, to me.
The quick start guide has gotten shorter now than it was and makes no mention of Boot Camp and FileVault2 - I thought there was.