Audio out of sync after encoding

I'm hoping someone can offer a suggestion.  I've encoded my sequence 4 times now and every time the audio is out of sync with the video.  The sequence is about 2 hours long.  It was shot on a HD flip cam, , 1280 x 720 (1.0) 30.00 fps, 44100 Hz.  The sequence is HD 1280 x 720 (1.0), 29.97 fps, 48000 Hz-Stereo.  They are the exact settings I've been using to make these videos for the past 5 months since upgrading to CS5, and this is the first time I'm having this issue.  I usually make 30 minutes videos, this is my longest yet.  
I've definitely had this happen before with cs4, but was hoping the upgrade to a better version as well as better computer would do away with these encoding issues. I dont' know what other info you may need, but I'm happy to provide more.
I'm exporting to window's media, NTSC Source Hight Quality, output 720x480, 48kHz, stereo.  Everytime I export it, the video markers only cover half the sequence.  I have to move them to cover the entire sequence.  Not sure if that has anything to do with it.
I'm at a loss.  Any suggestions would be so appreciated.
Jules

Thank you so much.  I did have problems with Encore, but I hopefully got that resolved.  This specific problem is audio out of sync in my media encoder.  I can't test the project beforehand.  It took 2 1/2 hours to encode and when I played the finished project, it was out of sync.

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