if everything plays off the Premiere timeline fine, then we can hypothesize that its an export issue.
maybe you could try exporting your work area only as an .avi file. i realize that you will still have to encode it in Encore, but atleast you could preview the .avi file before importing to Encore in order to make sure the file plays correctly in your windows media player. if it does than i guess you might be safe, if not there will be more exploring to do. you said “Then I export to Adobe Encore at 4800 (audio)”…you meant 48,000 right?
you might export the video alone and the audio alone and then place them on the same timeline in encore, as you had suggested, thats another good test.
ive never exported directly to encore, ive always exported to the hard drive then imported to encore.
i hope that helps.
Craig Davis
Color Bars Communications, Inc.
http://www.colorbarsvideo.com