odd but I've been going through the same thing. I am also going through orthotics adjustment so we can't figure out what it is. My PT (not Eric but the running one) wants me to chart when it hurts. Going upstairs/downstairs is bad and the flats on the bike is bad. It's only one foot and it's my dominate one.

The PT did say my ankle was tight and she did a lot of moving it around. It hurt to the touch only in certain spots and it sometimes hurt when she moved it but not all the time. Anyway today (the day after) it feels much better. It will be interesting to see if it's the bike or if it was the orthotics. She changed the orthotics a bit.

I guess that isn't much help. Chart it though like where it hurts and what you were doing when it hurt, that way the PT can narrow it down unless it's something obvious.