Bounced audio is seconds shorter, but not when re-imported...

Hi - I'm scoring to video (.mov file).  I have hits in specfic spots, and my client was complaining that things weren't lining up.  The time - let's say at :45 looks correct on the video, but when I bounce the audio and play it back in Quicktime, that hit is almost 3 seconds sooner.  I assume my client is having the same timing issue. 
I have re-imported the audio into the project, and it's accurate!  I've started a new project, and the hit is again in the correct spot.  What gives?  Inside Logic, the timing is correct, outside it's shorter. 
iMac, Logic 9, OSX 10.8.5

Hi, Steve. After you bounce your mix to an audio file, what next?
In other words, if we take it step by step...
1. Your client sends you a video file in mov format.
2. You load the video into Logic and create your score.
3. You bounce the audio mix of your score to an audio file.
4. You close Logic.
5. You now have a new audio file and the original video file. They are seperate things.
6. At this point, how do you marry the audio and video together for playback for your client?
To me, it sounds like that is the crucial question.

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