H.264/ACC mp4s for iPhone - What's different?

Question

I want to learn how to MANUALLY set up my own H.264 videos for iPhone, but
I'm having trouble determining why I can't custom encode video as H.264/ACC mp4 and get this onto iPhone.
from the tech specs (just H.264 stuff):
Video formats supported: H.264 video, up to 1.5 Mbps, 640 by 480 pixels, 30 frames per second, Low-Complexity version of the H.264 Baseline Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; H.264 video, up to 2.5 Mbps, 640 by 480 pixels, 30 frames per second, Baseline Profile up to Level 3.0 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats;
When I use QuickTime presets to encode to iPhone, works great. Same with most 3rd party apps... encode to iPhone, works good. But none of these options even allow me to see exactly how the video is being encoded (detail summaries are available, but I want to see how to set this up MANUALLY without using the preset).
Even when I use QuickTime or Popcorn, with my own custom settings, say, H.264 with 1000kbps, at 640x480, QuickTime will play it, iTunes will play it, but when I go to sync, I get the message that the video is incompatible with iPhone (but it should be compatible!... its H.264 with the low complexity version of the Baseline Profile).
VLC has transcoding ablities (nice software!), and encodes H.264 w/ ACC mp4s, and I have now tried dozens of times to get anything out of VLC in H.264 onto the iPhone (again, result works in QT, and iT, but refuses to sync to iPhone).
What, exactly, is special about encoding for iPhone, that one can't just follow the specs and expect it to work (like it works well for mp4v?) If my video is encoded properly (AFAIK), even if I match the specs when encoding custom, say, with QT, using what QT would use with its iPhone setting, it still doesn't work.
What is different about the videos that work with iPhone, and the videos that, by all appearances and specs, should work, but don't? What is special about iPhone video encoding that isn't obvious from the specs Apple advertises?

Answer 1

If you want to encode video with H.264 for playback in Flash Player on the Web, consider rendering and exporting to an F4V container.
There's a lot of information about H.264 and F4V files in the "Render and export a composition as an FLV or F4V file" section of After Effects Help. That page also links to several resources that go into much more detail about compression options for H.264.
Alternatively, if you are going to use a separate, third-party encoder to create your H.264 files, then don't encode to H.264 from After Effects; rather, create a losslessly compressed master movie that you then run through your encoder.