Unable to login to El Capitan Macbook Pro after booting, works after waking from sleep
This link https://support.apple.com/en-au/HT202842

Talks about how to force people to enter their passwords twice in order to login. It doesn't say so, but I read into this that it's possible to have a different password for unlocking the machine and for logging on. 

I also remember once having a problem where the machine was asking for both passwords even though I had autologin enabled and the passwords where the same. I think I had to reset the PRAM or something like that. Sorry, was a while ago and haven't had the problem since. 

Some other links that may give you clues:

https://discussions.apple.com/thread/6626285?tstart=0
https://support.apple.com/en-us/HT204837