Removing and re-placing the work benches fixes this for some but not all of my villagers. I'm not sure why.
I had this same problem in RC2. I had to remove and re-place all the beds to solve it. I found the villagers were not going to sleep and the beds were marked as occupied.
Pure vanilla.
Removing and re-placing the work benches fixes this for some but not all of my villagers. I'm not sure why.