When capturing HDV with autoconversion to CF Intermediate and automatic scene splitting on, the audio is longer than the video in the clips.

Is this normal?

Yes. It is related to the way mpeg is storing audio. When transcoding we present all the video and audio data (even if audio can be a slightly different length.) This causes no issues.

Thanks David.

But why does the mismatched length only occur when I've turned on "auto scene split" in HD Link?

That gets too technical. It is all about the MPEG transport stream structure.