QT no longer converting audio from AVI correctly

I am using QT Pro and QT Player on a Mac Pro Gen 1 and found recently that the audio doesn't convert properly when exporting to iTunes. What I find odd is that I can convert the same AVI files on my MBA without any issues. The only major difference being the the MBA is running ML wheras the Mac Pro is running Lion.

The AVI files play fine with both players but the resulting iTunes file sounds like its chopping out the audio by about 50%. The video file is fine just the audio is the problem.

Has anyone else come across this and/or have any remedies?

Could it be some codecs have become corrupted??? If so, how and which ones to replace?

Thanks in advance.