try turning off the texture filtering settings. if for some reason you are using save states, even if it is this early in the game, make a real memory card save and try loading from that instead.
high cpu usage rates like that are normal, unless you are actually having performance issues regardless of how you have things configured it is nothing to really worry about.Though I don't think it mattered I switched my bios to 1001. I also changed a few video settings and suffered through the intro again (can't skip it). Good call on the save state thing...
It looks like it's working now! Oh, and I turned on a cpu monitoring gadget to watch my cpu use and my cores were hitting 100% (was watching the colbert report at watch.thecomedynetwork.ca at the same time. I really need an upgrade...)
I turned it off and the audio glitching / skipping went away.