Works in Itunes, not ATV

I've been using Handbrake to encode some home movies from VOB files to MP4. I've tried several settings that work in Itunes but the ATV won't recognize them. Has anyone else seen this?
I am using the Windows GUI version.

If someone could post setting on Handbrake that they would definitely work, I would appreciate it.As indicated above, it difficult to provide specific advice or settings whithout knowing what you are trying to do. For instance, are the target files meant to be both iPod and TV compatible orcompatible with just the TV device. If both, which profile ("Baseline" or "Low Complecity") are you targeting. If "Low Complexity," what version of HandBrake are you using -- the public release or a beta compile -- or do you have alternative software available? To maximize video data rates, we need to know what dimensions (or width and aspect ratios) you are targeting. Are you trying to maximize quality at the expense of time or are you seeking fast encodes and not worrying as much about the quality? Basically, you want to use the MP4 file container, H.264/AVC codec, and the X.264 encoder. All other setting are dependent as mentioned above and require specific information from you or a list of settings which would give us at least some idea what your are shooting for as an output file.
I know ATV lists settings but Handbrake has more options so maybe its something I chose incorrectly.AFAIK, the only options available to yo in the public release are the "Main" profile which is only good for TV and the "Baseline" profile which is only good up to 320 x240 for dual purpose files. For "Low Complexity," you would likely have to use alternative software unless the beta HandBrake project now includes this specific profile. Video data rates for dual purpose files are limited to 768 Kbps for "Baseline" profile and 1500 Kbps for "Low Complexity" profile. The "Main" profile usually requires video data rates in 1850 to 2300 Kbps range depending on width, aspect ratio, and frame rate (i.e., from 640 x 266 2.40:1 or 640 x 272 2.35:1 through 640 x 360 16:9 or 720 x 400 16:9 and on to 640 X 480 4:3 aspect ratios and 23.98 to 30 fps.) And if you plan to push files to 480p30 (854 x 480 16:9, 854 x 363 2.35:1, or 854 x 356 2.40:1, then your video data rates may need to be as high as 3.0 Mbps or thereabouts.
Screen shots from Handbrake would be great.Here are typical settings for an old NTSC encoded 4:3 TV Show that approximate CAVLC settings. (Note: Deinterlace is also switchewd on.):

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