It seems like a bug honestly, but maybe it's by design.

Apparently you can't get either type of rested buff if you use the Lover's Guardian stone that provides the +15% increase to all skills.
As a result stick to Thief, Mage, or Warrior + Rested/Well Rested for better increases in skill.

I noticed this while playing my Thief and had switched from the Warrior stone to the Lover stone and couldn't figure out why the heck I couldn't get the rested bonus anymore. Went back and picked the thief stone, slept in bed, and voila, could get the bonus again.