Analyze Audio is still a bit flaky with certain video types, I believe (or last I heard anything about it, it was):
http://yabb.jriver.com/interact/index.php?topic=93236.0I know Krazykanuck was having trouble with DVD rips (full ones with a folder full of IFO and VOB files), and he provided Matt with a sample, but I don't know if it got fixed.
If you're having trouble, the recommendation is to do them in small batches. You'll probably find that it is a particular type of files that is causing the lockup. If you can, use DropBox or WikiSend to post an example file in this thread, and Matt or Hendrik will probably take a look.
Also note that the message that "Media Center has stopped responding"
does not necessarily indicate that it is crashed.
As is explained in the Troubleshooting Guide, this can mean that MC is just really busy and it can't update the UI thread. Often patience will allow it to "unstick". Analyzing Video files can be pretty resource intensive, depending on the original source file type. If you find a particular file type that causes this, but you find that it does eventually start responding again, please report that as well.