Because of the time delay in the digital portion of the HD Radio audio path, the analog audio component of the hybrid signal has to be delayed to match the digital. When the alignment is just right, the transitional blend from analog to digital or back can be almost transparent. However, if the alignment is off by even 1 millisecond, listeners will hear the transition. Likewise, a difference in audio level between the two signals can cause problems.
Brian Beezley has documented the audible effects of misaligned time delay and mismatched audio to show the effects. He has even written a small program to compare the analog and digital signals so the best alignment can be found. His program runs in DOS or from the command line. It uses the computer's sound card and an HD Radio tuner than can split the audio into analog on one channel and digital on the other. The results of the program indicate time alignment, level differences and phase relationship.
Beezley's site has lots of useful information, so look around while you're there.
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