Audio Warble/Distortion

We have just migrated our FMS install and application to a new quad core linux server and have found that the audio is now distorted and warbly even though it is still using the original files and application that worked fine on the old sever.
We are running a live stream from a server side playlist and the audio seems to warble and distort all the way through. When the flv files are played localy though they sound perfect, it is only when they stream that they are distorted. They are encoded to 400kbps video bit rate so I dont think thats the issue.
The stream video also sometimes skips a lot and then fast forwards really quick as if its trying to catch up. The audio is a main constant issue though.
This is a link to a video screen capture of the problem so you can here it.
http://www.matt-adamson.com/fmsExample.wmv
Does anyone know what might be causing this as we are totaly stumped and have a closing deadline.
Thanks!

I have just noticed something, when one person is connected to the stream the admin panel bandwidth monitor spikes up and down every second e.g. one second up the next second down, alternating constantly. Maybe this could be causing the problems with the audio and playback but I dont know why it would spike like this?
Is this normal?
Heres a screen grab.
http://www.pinstripe.tv/peak.jpg

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