It could be your firewall blocking certain ports. Go into the settings of that and check if MSN is allowed.
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I found this on another site:
A friend experienced a delay with her instant messaging. After trying many different thing from uninstalling, reinstalling to deleting things from registry to do a clean install we finally narrowed it down.
It was the FIREWALL
She has Norton Internet Security 2004
We had to go into Personal Firewall>Programs>look for your messenger and set it to automatic
This created 18 different firewall rules compared to the one before.
After doing this her msn messenger was back to normal
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Maybe something similar is happening to you. Or you are using so much system resources that there isn't enough left for the audio. If this is the case try not to run too many other programs whilst doing Video/audio chat.
Edit: yw