For what it's worth, this worked for me as well. This should be tried before anything else since it changes absolutely no settings or files.
Turn off SuperSU (Settings -> More - > Application manager -> All -> SuperSU -> Turn Off)
I had this problem for a looooong time. Thankfully, I seem to have discovered a solution for those still encountering this issue.
Turn off SuperSU (Settings -> More -> Application manager -> All -> SuperSU -> Turn Off)
Reboot into Safe Mode ...
I have beat my head against the wall until it was bloody trying to encrypt my phone. Android suggests that all one needs is a fully charged phone, a strong password, and an hour or so available for the seemingly easy task. Unfortunate...