Random Flinching/Reflexes

[Alreiger]

I do have a problem with my right ankle. If I run on it, sometimes it will just give way and leave me in excruciating pain.

Hmm, that usually wouldn't have any affect on your upper body muscles unless a nerve got crossed (I don't think that's even possible). The only real answer I could give you based off what you've told me, is that you've got a nerve / muscle condition, now it's up to your doctor to answer your problems.