My Roku 3 remote headphone jack suddenly stopped working between one session and another after I had unplugged the roku set. I tried unplugging and replugging the headphones. I tried another set of headphones. I tried the volume button on the side. No luck.
Searching online revealed nothing about roku headphone jack problems and neither did a search on the roku site.
So, I did the most basic thing. I removed the batteries and put them back in the remote. It worked. Somehow the remote just needed to be reset.
UPDATE: The batteries were wearing out, so I replaced them too.