Audio Sounds good in SP and bad in FCP

Hi,
I preface: Recently i did a clean up of system with prefernce manager and pro maintenance tools.
I just sent an audio file from FCP to Soundtrack Pro (SP) to get rid of clicks. Sounded great in SP but with more clicks than it originally had in FCP. Never had this problem. I'm sure it's related to the fact when i went to export the file from SP after taking clicks out it asked me if I wanted to Reference Source Audio or Include Source Audio. I chose Include Source Audio even though it said in the box that it wouldn't play correctly if I didn't reference source audio, but it said i could change the setting in preferences back to the default. I did change it back to reference source audio, resaved and exported and it still has all those clicks in FCP.
Any help is appreciated!
Thanks,
joe

Hi Mike,
Thanks for your help. I played it in i tunes and fcp today and it sounds good in both, but yesterday it was cracking throughout. I don't understand. Bizarre.
Thanks again!
joe

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Hi all,
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http://www.youtube.com/watch?v=8Wz09yHXheU
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Try #2 and #3 in link below. If neither work, you most likely have a hardware issue.
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To be effective, it's best to have the noise floor at or below -42dB and vocals riding around -15/18dB to get that clean separation expected from a treated room.
Look for at least a two second gap in your recording that has just the noise in it to capture a sample (right click, capture noise print). I generally record 10 seconds of the rooms ambiance just for this purpose.
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