I might try it again with larger beets (maybe golden instead of red) and vegetable stock in place of the water. (marthastewart.com)
Remove the onion pouch after about 30 minutes (slices should be tender and very lightly browned), and allow beets to continue cooking until easily pierced with fork, about 50 - 60 minutes (could be more for large beets). (connoisseurusveg.com)