I know this is an old thread, but did you ever resolve this issue? I've been having the same problem for months, and have wasted a ton of time searching for an answer and have yet to find one.
Often when I take photos with the iPhone some of the photos do not get to the Photo Stream. For example, I took 12 pictures in the same location within an hour (but not in rapid succession). The first 5 are in the Camera Roll and Photo Stream. The next 7 are only in the Camera Roll. I did not change any settings. This happens frequently and happened before and after the most recent update. iPhone 4s.

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