I do think this is a player limitation, we have seen this before. HLS (cupertino) streaming does not handle short clips well.
With this command, copied from your post above, I get one chunk in the chunklist:
If I set the Application.xml /HTTPStreamer /cupertinoChunkDurationTarget to "1000" I get 2 chunks, but they are awkward because Wowza will only break on key frames. That setting is a "target".
ffmpeg -i sample.mp4 -ss 3 -t 10 -profile:v baseline -level:v 13 -an sample10SecBaselineLevel13NOAUDIOv2.mp4
What is the most recent encoding? And what cupertinoChunkDurationTarget ?
In any case, I think this is a player limitation. I don't have an iOS 5 device handy to test, but if it was different in iOS 5 I don't think it is because of Wowza