i got frustrated when i first installed SF:Anniversary Collection and found out that even if i have 2 controllers plugged in, one of them still doesnt work, i found that kind of odd but today at a friends house i found a way to solve that problem.

when you start HDloader with 2 controllers plugged in, one will have the analog light on and the other one wont, switch on 2p's analog mode and then start the game, you should see versus highlighted in 3rd strike as well as Hyper SF.