Dug into this a bit more and learned how to find Codec IDs, results of some tests:
Streams:
mp42 (isom/mp42)
mp42 (mp42/mp41)
mp42 (mp42/mp41/isom/avc1)
Doesn't stream:
mp42 (mp41/isom)
isom (isom/iso2/avc1/mp41)
Umm so I don't know what it all means but the ones with mp42 in the brackets stream but the ones without don't? I'm guessing mp42 is an newer format with better streaming handling?
Is there anything that can be done about this though? Seems many of my users are uploading videos encoded with mp41 and then are unhappy about the streaming support. Would this be a feathers question or an Air one or just some known fundamental software limitation?