My experience with ac3 is, you need to make sure the levels of your volume do not at anytime exceed the normalization level. Mine is set to about -3 db. Even though I normalize the sound and expect it to be -3db or lower, it doesn't always work perfectly. So you can either go in and cut down the spikes by a db or two or you can put a "volume" envelope on the whole project and lower everything by enough to at least bring the very highest point to about -0.1db lower than -3db.
My problem is that when I render to ac3, I either get nothing or what sounds like a backwards recording if my volume is too high at any point.
This is how I get around the problem, but have not heard anybody else address this.