You should give this a try:

defaults write /Library/Preferences/com.apple.loginwindow DisableFDEAutoLogin -bool true

This will disable the FileVault autologin and show you the normal login window after authenticating for FileVault.

Above post (defaults command) is definitely relevant. That said, I've found the config profile does not always load recently with 10.11.2 and Profile Manager-generated (JSS-generated doesn't work at all). I've installed via APNS and manually. It seems we need a triple login (more often than not) these days to grab our 802.1x/WiFi. Perhaps something environmental as well introduced here.

edit: just a note that I've been using -bool YES/NO to control state

HT202842

defaults write /Library/Preferences/com.apple.loginwindow DisableFDEAutoLogin -bool YES

A few months ago, we used 802.1x with username/password and had similar problems. In addition, waking up after sleep caused the WiFi in nearly all cases to fail. Among with other problems, we decided to switch to certificate based EAP-TLS authentication. All problems we had were instantly gone with this.

BTW, using "yes" or "true" in the defaults command is the same. You can use both of them.

@m.entholzner

When you were seeing issues with 802.1x, did you ever notice the config profile fail to load/register at Login Window (e.g. Network Interface selection doesn't appear ... only User/Password fields). That's new to us.

Reconnect on sleep went away for us with 10.11.x. Only took a OS release cycle.

YES/true NO/false ... yeah, shouldn't matter. I probably had a typo at one point and became superstitious. :)

no, this is new for me too. There were only issues with the connection itself.

@m.entholzner

Do you have any documentation or write up on going cert based? Do you mean device cert based? Or?

Thanks in advance.

@jkosowsk @ChrisLeeSSD

@bwiessner: yes, we are using machine AD certificates. there is a good documentation on afp548:
https://www.afp548.com/2012/11/20/802-1x-eaptls-machine-auth-mtlion-adcerts/