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The audio ID is not the same as the audio PID. The audio ID is the one shown in the audio box of the info dialog. For transport streams, it is always 0. If you specify 0 as the audio ID everything will work as expected.
The users manual does state in the "Select Tracks" section that the audio ID is always 0 for transport streams, but I'll add that to the Analyze Sync section as well.
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