So if i get you right, you saying you take "live" feed from Flash Media Live Encoder (I am assuming its FMLE as i have not heard about product called Adobe Live Medi Encoder) and then publish it to FMS and record it on FMS using some server-side code of your own and while recording you choose "mp4" as format - did i get you right? If yes - can you try below stuff I am not sure what is the reason for post production stuff but probably before you use it post production - may be you can post process it using f4vpp and then pass it to CS4 and see if it helps resolving the issue.
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