Hi Hongjun,
Sorry for the delay, it was a holiday here yesterday. Thank you for the complete information, this is extremely helpful, particularly the contents of the pushPullSetup.xml file. There seems to be a bug you are experiencing, and I have passed this information on to the team. My initial guess is that the transcode command you are using is "fine-ish" and works based on the parsing from the command. It then gets saved into the config file. When the EMS restarts and reads the config file, I believe it determines the command to be incomplete and removes it from the config. Again, I am guessing based on what i see here in your posts.
One thing I would recommend you try while you are waiting for us to evaluate it further: make sure to set audioBitrates and videoBitrates. Technically, the transcode command should not actually do anything if you don’t set one or both of those values. (for example, only setting videoBitrates would mean the result would not have any audio) You can even just set them as the following for an initial test:
audioBitrates=copy videoBitrates=copy