Trimmed podcasts play correctly in iTunes but not on ipod shuffle

There's some short podcasts from NPR that have commercials at both the beginning and end. They're almost as long as the main content. I've been able to use the "Batch Trim Start or Stop Time (Seconds)" script from Doug's Applescripts for Itunes website to trim 15-20 seconds off the start and stop times. It works when I play them in iTunes, the podcasts start and stop exactly where they're set. But if I sync these trimmed podcasts to my iPod Shuffle then either the start or end time is ignored, or the podcast just abruptly ends in the middle.
Any ideas what's happening?

Anyone know why the start and stop times aren't respected on the ipod but are in iTunes when using the batch trim script?

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