Keith--most likely the rot was caused by too much fertilizer, too often. You don't say what you were using but generally what's recommended for lilies is 5-10-5 to a balanced 10-10-10. Lilies don't require as much feeding as most fast growing annuals do. So, fertilizing too much, especially one with high nitrogen can weaken the bulb and make it susceptible to attack by soil borne pathogens that cause basil plate rot.
Follow Jason's recommendations for feeding times; it's a good one, although the fish emulsion can be substituted with a light application of 5-10-5, if you wish.
Be sure all your pots have good drain holes and don't forget to tip your pots sideways in winter for drainage because if left upright, those drain holes freeze shut resulting in a pot of freezing/thawing/freezing/thawing mud come the spring thaw. That will kill your bulbs, for sure!
