What you're saving from VRD is a PS (program stream) rather than a TS (transport stream) file. The original file from the TViX is also a program stream, as opposed to the originally broadcast transport stream. TS can contain many audio and video streams, whereas a PS contains only a single program (which may have several audio tracks).
If you see different results when playing the original TViX and VRD files, it may mean that the TViX has misinterpreted the original TS and included extraneous packets or that there is corrupt information that VRD is able to discard/correct.
From the symptom that you describe, my guess is that the station is actually changing the audio PID or format during the program in question, shortly after it starts and VRD is clever enough to sort that out and create a single audio track in its output. One way to test that would be to begin your recording of that program several minutes after it starts and see if the audio is more reliable when you play that back.
Otherwise, you can also use TSReader to examine the before and after VRD files and perhaps discover what is the problem source by looking at their respective PAT/PMT structures.