i had ZERO of the problems that you are listing... if you are on a "fight sequence" and joel is not running when you press the run button, then i really feel that youre controller must be busted... is the only logical explanation for me since it always worked in each of my 4 playthroughs.
also i expect you already know that there are some sequences (with no combat) when characters are simply talking and you cannot run, for the sake of "pacing" (maybe those are the sequences where you dont understand why you cant run?).
i also never had a problem with the melee combat so... yeah cant help you with that either.








