Why won't some of my MP4s stream to Apple TV (or iPad) via Home Sharing?

Question

Hi all. I've been converting my DVDs, HD-DVDs, and Blu-rays to MP4, using MakeMKV and then Handbrake 0.9.9.5530 64-bit for encoding. I have been intending to play the files on my iPad, both transferring to the device and streaming via Home Sharing. I also want stream these via Apple TV (3rd gen, Model A1427) in the house via Home Sharing.
All the files sourced from HD-DVDs & Blu-rays seem to work fine. However, more than half the DVDs I've converted -- using the same Handbrake preset I've been using for the BRs -- will not play back on the iPad, or streamed to the iPad, or streamed to Apple TV. The files will copy to the iPad, but for both device playback and streaming, I get the error message "The operation could not be completed." On Apple TV, it's "An error occurred loading this content, try again later."
The files will play in iTunes for Windows, and they will play in VLC. (Files bought from the iTunes Store also stream fine.) There is no metadata in these files, but I am manually adding a poster image once I drop them into iTunes.
It seems pretty clear that this is a problem with the file itself, but since the only issues I'm having involve streaming, I reset my router for good measure. I restarted the Apple TV and quit all the apps on my iPad before restarting it, too. I've also made sure the firmware on all devices is up to date. None of that had an effect.
I compared a DVD rip (Bill & Ted's Excellent Adeventure) to a BR rip (Independence Day). Both feature exactly the same bitrates & sample rates for video and audio -- according to the Windows Properties -> Details tab, Data rate is 1499kbps, Total bitrate 1659, 23 frames/second, 2 stereo audio channels at 48KHz. The only difference is the BR frame size is larger (1920x812), and of course the run times & file sizes are different. But the bigger file plays fine, and a lot of these smaller files do not.
MP4s from DVDs that will stream: Toy Story, Dead Again, Clue, School of Rock.
MP4s from DVDs that won't stream: Ocean's Eleven, Escape from New York, Galaxy Quest, Robocop (Criterion). Shaun of the Dead, Team America World Police
Again, these were all converted on the same PC with the same software and same settings. If there's a common thread among the source material of the MP4s that will play and won't play, I don't know what it is, but I figured it would not hurt to list it. 
My Handbrake settings are based on Handbrake's AppleTV 2 preset, with the following modifications:
Avg Bitrate 1500, 2-pass, no turbo 1st pass
Framerate: 30, Peak
Optimize:
x264 Preset: Very Slow
H.264 Profile: High
H.264 Level: 3.1
Container is MP4, as is the file extension. (Since dragged-and-dropped MKV files default to M4V in Handbrake, I select MKV then re-select MP4 from the Container drop-down before adding to Handbrake's queue.)
Someone suggested I simply change the file extension to M4V, so I tried it, but that did not fool any of the stream devices.
I have been testing the output MP4 files on my PC as I go, and once they played fine in VLC after Handbrake, I have been deleting the MKV files. I can go back and rip them all again if I have to (these are all from DVDs I personally own), but obviously I'd rather not do that! So my questions now are:
- Could this be related to the audio stream? I've been opting for the DD 3/2.1 stream whenever possible when ripping, and letting Handbrake mix it down.
- If I run the MP4s through Handbrake a second time with a different setting, will it do a pass-through convert instead of a full re-encode? (I don't want to shrink the video if only the audio needs attention.) If so, which setting should that be?
- Is there a way to repair these MP4 files without completely starting over with a fresh MKV?
- If I have to start from scratch, should I go with Constant Quality over Average Bitrate?
Hopefully someone can spot my issue based on this description. I'm happy to send you my Handbrake settings as a .plist file and offer any other info I can, as I'm stumped as to what went wrong. There has to be a logical reason. Thanks!

Answer 1

I've continued tests on different films, and tried my entire collection. I've found about two dozen that will play fine on the PC, but will not cooperate when streamed to either Apple TV or my iPad. I tried several more tests with the audio, and that turned out not to be a factor -- I could not replicate that on another test.
I wonder if something in the header of these files is corrupted or a flag is set incorrectly or something along those lines, as the data appears to be fine -- it's just not "handshaking" with my streaming hardware and/or the Apple Home Sharing code that powers it.
Is there any way for me to "scrub" these files and amend their headers, or get into the file and tinker with that info by hand?