It sounds like the foot needs to be strengthened.
The construction of your shoe has been making the correction for you not your foot.
Do you have an arch?
Are you missing internal rotation?
Here are a couple episodes that start to address it.
Episode 54: Pinchy Ankles and Weak Feet
Episode 07: Bro, Your Navicular Bone Dropped
Episode 293: Haiku Winner, Travel Ideas, And Your Feet
Rebuilding Your Feet With Brian MacKenzie
Rebuilding The Feet, Part 2
Rebuilding the feet, Part 3
Pro Episode #3 – The Flat Feet Solution
Daily Rx Saturday, August 17th, 2013