Can't Sync Some Video Files

I have just spent the last few weeks using HandBrake to rip the video files off my TV Seasons and movie DVDs and importing them into iTunes. I used the same exact rip settings for all my DVDs. There are some that are able to be synced to my iPhone, while others result in iTunes telling me that "Video Name" was not copied to the iPhone "iPhone" because it cannot be played on this iPhone. Now, this is really strange because all of my videos are the EXACT SAME video format. The only difference I can see is a few kbps in the total bit rate and a different video dimension...
*Specs of a file that WILL sync:*
Kind: MPEG-4 video file
Bit Rate: 159 kbps
Profile: Low Complexity
Channels: Stereo
Encoded With: HandBrake 0.9.2 2008
Total Bit Rate: 1159 kbps
Video Dimensions: 853x356
Video Codec: MPEG-4
*Specs of another file that WILL sync:*
Kind: MPEG-4 video file
Bit Rate: 159 kbps
Profile: Low Complexity
Channels: Stereo
Encoded With: HandBrake 0.9.2 2008
Total Bit Rate: 1118 kbps
Video Dimensions: 628x478
Video Codec: MPEG-4
*Specs of a file that WILL NOT sync:*
Kind: MPEG-4 video file
Bit Rate: 159 kbps
Profile: Low Complexity
Channels: Stereo
Encoded With: HandBrake 0.9.2 2008
Total Bit Rate: 1154 kbps
Video Dimensions: 853x478
Video Codec: MPEG-4
*Specs of another file that WILL NOT sync:*
Kind: MPEG-4 video file
Bit Rate: 159 kbps
Profile: Low Complexity
Channels: Stereo
Encoded With: HandBrake 0.9.2 2008
Total Bit Rate: 1153 kbps
Video Dimensions: 628x478
Video Codec: MPEG-4
As you can see, there isn't much of a difference in the files that will and will not sync. I know that the files aren't corrupt because iTunes has no problem playing them, it just can't seem to sync it. Can anyone tell me why this is happening?

Do you have the "show only the synched items" box checked? It's on the summary page when you have Apple TV selected under devices in iTunes. I had this problem and it took me a while to see it...now if my Apple TV would just stay connected to iTunes......or if someone could help me downgrade to 2.0 I'd be golden.

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