From my limited experience in the game so far, all of the Enchantress runes that I have found were located in Fairy chests which are Uncommonly found throughout the Castle and possibly the other areas.
- Fairy chests are opened by completing challenges, a few to mention are:
- Kill all enemies in the room
- Take no damage
- Open in 5...4...3
- No fighting
- No jumping
- No Looking
After finding an Enchantress rune, the next time at the base camp area, in her shop you can purchase the rune you had found.