Just to add some confidence, I upgraded my Mugen 1.0 install to 1.1 before the final beta was even released and had no problems. (At least nothing that wasn't fixed by 1.1b1). Supposedly, people are managing to find problems with some 1.0 characters, but I can't recall any such thing. Generally, if there's an issue, it's some crappy Winmugen character using DOSmugen code that won't even run Mugen 1.0 or something similar.

Occasionally, you might run into something that needs fixing. I can think of two main culprits.
1) badly coded displaytoclipboard states : Just null them because you don't freaking need them
2) characters with states that use stagevar for a trigger : Generates a wrong version error. Just null that, too. It's usually the remnants of a character from a fullgame or something useless