Audio thrown off by Transitions

i have a section in my video where i have a baby crying ... and I am syncing the crying with the video .... ( the crying is from a seperate audio source ) ..
I have the audio matched ... but when i add transitions in between the clip ...it throws the audio crying off sync ...
I've read that doing transitions after syncing audio is a no-no ...
But if i wait to sync the audio after the transitions .. will the audio still match up ...?
Do i have to cut up the audio file to match each little clip ..?
HELP PLEASE ...!!!!!

I did something similar.
I made a "music video" for a friends band made up of live clips I've shoot, and one of the songs from their album playing over the top.
I was using the audio track to get things right and sync up the different clips and transitions so they roughly matched what was going on in the song.
Then I removed the audio track and re-added it and it was all great.
But when I saved it, and also uploaded it to YouTube, this one part at the end wne t out of sync.
Here's the video:
http://www.youtube.com/watch?v=pfUi-y-0dGc
You can see the part I mean, right at the end just before it fades into the live audio I kept in on the last clip.
I don't get why this happened when it was perfect before I uploaded it.

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