Multiplexing MPEG-2 and Aiff exported from compressor

I have been exporting MPEG-2 and Aiff files of of videos through compressor. I have been using Bit-Vice Helper to Multiplex them together for broadcast.
My problem is that on longer videos, the audio will cut out part way through the video.
Does anyone know of alternate means of multiplexing the MPEGs and Audio, or has anyone run into a similar problem and know of a fix for it?
Thanks.

Are you trying to create an MPEG2 Program or Transport stream? If so, Compressor 3 does this.

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