Quicktime .mov containers with multiple tracks not working on iPhone

Hello,
I have several .mov files (containers) that all include H.264 mp4 video tracks and AAC sound tracks.
Some of the .mov files only include one video track and one sound track, but some contain multiple, as I have joined a few clips together into one container. Each .mov file was saved as a Standalone file, so no reference files are needed.
All of them play perfectly in Quicktime and iTunes and all sync with both AppleTV and my iPhone. They also play perfectly in AppleTV, but my iPhone only plays files with a single video and audio track. If the .mov container includes more than one video track, the iPhone will play the first track and then freeze when it should transition to the next track. (Is this a known iPhone bug?)
My question is: Is there a way to merge video tracks and sound tracks within a .mov container without having to re-encode/export the file to an iPhone format?
The reason I do not want to export everything to an iPhone format is because I already tried that, and the total size of all the exported .m4v files is around 10 GB but the size of the .mov files is only 5.6 GB, yet I do not see any difference in quality. And my iPhone is only 8 GB, so I can't sync all of the files if I use the iPhone format.
I've also tried several different settings with iSquint, but the smallest I can get the files down to is 7.4 GB without compromising the quality, and that leaves very little space left on the iPhone.
Note: The iPhone is a 2G phone with the latest firmware.

I'm having the exact same issue with my iphone 4s.. I have a belkin wireless router with multiple other devices connecting effortlessly every time. I have my old iphone 3G, and ipod touch, and 2 laptops connecting with no issues. I am receiving the same error message as you. Lame.. If this doesn't resolve itself soon, I am returning the iphone 4s.
TJ

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