Pretty sure that's not the issue since I'm playing on a Madcatz SFIV tournament edition stick(the 20th anniversary one to be specific).It could be that your stick is badly designed. I used to get pain until I switched to a better stick. What stick/parts do you have?
and what are you used to playing on? Pad? keyboard?
Blew out my finger again this weekend. It's really perplexing since it's just my right index finger and that's honestly the finger I use the least.