Rule of thumb is to Un jailbreak it before taking it to an Apple store. They could just look at it and say, Sorry cant work on it, as they really aren't supposed too. Of you get a cool genius they might. Keyword is might.
Our Apple store told me they have a computer just for this. You restore it if needed before they fix it. It's cool that they set aside a computer for this instead of turning us away. The genius advised that it's very common so they don't really care now.