Mpeg2 for broadcast

i think I have a fairly simple problem here.... hopefully.
I am trying to deliver a multiplexed mpeg2 file for broadcast and every time I use compressor to do so my audio comes out incomplete. usually at the head the tone cuts in and out. I have submitted many mpeg2 spots to my client and they always come back with some sort of QC issue, such as audio cuts out or video interpulated. I need to find out a fullproof way of exporting a mpeg2 file for broadcast. the source footage that was cut in FCP6 was HD 1920x1080 at 23.98 then ultimately down converted to 720x480 29.97. once it is ready i export from FCP6 using compressor3. I choose apples mpeg2 program stream settings and choose extras then click on the mutiplexed box. once the file goes through compressing the result is a 640x480 mpeg2 file with spotty audio. for the life of me I can not understand when the file comes out 640x480 and the audio cuts in and out. anyone able to lend a hand in this???

Don't worry about the 640x480 resolution. That is the dimensions of the video in square pixels (which computers use), which is the same as 720x480 rectangular pixels (which NTSC uses). The audio is much more concerning.
Are you using 48 KHz audio in FCP? Or are you bringing in some tracks at 44.1 KHz?
Finally, you might consider using BitVice Helper Multiplexor, which is free and will take separate audio and video and multiplex them for you.

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