Be sure to import clips via the "Browser" window, not just "File > Import". The Browser will do a better job of interpreting the type of audio and video formats you are working with based on metadata and file structure found during import through Browser. Hope this helps
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Also try deleting the Media Cache files. PP will rebuild them when you open the project, and sometimes this corrects some issues.
Did you trim this clip in Premiere Pro? If so, you may have trimmed it at a high peak on the waveform. If this is the case, expand the timeline and track height as large as possbible and place the trim at the point that the waveform passes through the "0" line. Audition has zero crossing alignment for trims, this is not a feature in PPro as of yet.
Yes, non-Zero-Crossings can introduce "pops," as you mention. I have requested that same Audition Cut on Zero-Crossings function.
Often with the Timeline set to Audio Units, Snap OFF, and some tight editing, a non-Zero-Crossing glitch can be eliminated, but that Audition function would be wonderful.
I FIXED IT! Well, Adobe did actually. Right after posting this it occured to me that I hadn't updated my Adobe Suite. It was a clean install on Windows 8 and so I updated the whole suit. I didn't get to try it until today, was in Nashville and weekends there are hard core! Anways, it's all perfect now:) Thanks