Pulling your credit reports as part of an application proccess would count as part of a background check wouldn't it?
I would think if so, they'd have to get you to sign something stating that you're allowing them to do a background check and when you sign it you should let them know that you had CR frozen due to security issues and ask if that's part of their background check.
And then you can go from there.
Think the best thing would be to contact a human resources person at the company you're applying to and ask them.