Just sounds like the ankle isn't gliding properly - like you have some bones out of place, which isn't all that uncommon. I would recommend seeing a good manual therapist and they should be able to get it squared away pretty quickly.
In the meantime, I would suggest doing things to "decompress" the joint before, during and after stretches. Standing, just shake the ankle out - sometimes you'll get an audible pop from doing just this. Sit and cross the right leg over the left and just manually rotate your ankle in both directions, trying to relax the leg and foot as much as possible, and gently pulling the foot out away from the leg as you do. Dorsiflex and plantar flex it with the hands as well. Basically just trying to create space in the joints while moving through all ranges of motion.
I would do all that before any stretching, and then repeat after stretching. Shake the ankle out in between sets of a given stretch.
Good luck and let us know how it goes.