Mpeg-4 wont play in latest itunes

I converted some dvd files to mpeg-4, and it plays in windows media player, nero, my IPOD, etc, but NOT in Itunes/Quicktime (they both use the same player). In those two, audio comes out, but no video, just a black screen (I tried some trouble shooting from apple, i.e., disabling some directx features, but now only white screen).
Over a year ago I did the same encoding, and it gave me mpeg-4 files that still play in Itunes. In that player, if I click info, it displays "video codec: h.264" for the files that do play normally, and "video codec: mpeg-4" for the bad ones. I have the latest version of itunes/quicktime.
Can someone please help me with the heck is going on here? This is really frustrating...
Thanks

*What video content works with iTunes and iPod?*
Video content purchased from the iTunes Store.
QuickTime and MPEG-4 movie files that end in *".mov", ".m4v", or ".mp4"* and are playable in QuickTime Player.
Video podcasts.
http://support.apple.com/kb/HT2729#

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Mpeg-4 wont play in latest itunes

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