I had the same exact issue. I am using El Capitan 10.11.1 with my late 2015 27 inch iMac. I didn't like the lightning port rechargable magic keyboard that arrived with it... so I paired my old wireless mac keyboard (the one that uses two AA batteries). I enabled FileVault, and several days later I restarted my iMac, only to find that I could not enter my password. The recovery process was of no assistance either, due to the fact that the computer would not connect to my original Apple wireless keyboard. I found a wired keyboard in my closet that belonged to the last iMac I owned, which was the old school lime green iMac from 1998 (which still works - amazing!), and plugged it in. I was able to restart the computer using the menu prompts on the upper left of the screen menu. Upon restart, I was able to enter my password and get back into my iMac.
Hopefully this helps. Im hoping I can find a fix for this so I don't have to disable my FileVault.