I had problems with a xvid encode that had AC3 5.1. (Played via WMC, xbox 360 extender)
I encoded the audio to AC3stereo but still had slight stuttering.
I look at their specs and it seems to me it is mp3 only for xvid .avi For h264 it is faac stereo only. But also I think the problem only occurs with encodes with high resolution. So AC3 audio and high resolution, 720 or above, then stuttering occurs. It happens with HD tv rips and some high quality movie rips.
http://support.microsoft.com/kb/945416