Mp3 opened in iTunes has sections of low audio signal

I am responsible for lecture recordings which are recorded as AIFFs then run through iTunes to output 64k mono mp3's / podcasts.
Recently an mp3 file sounded fine when played with Quicktime player but when opened in iTunes portions of the recording sound very faint.
The podcast of the lecture also has the same faint portions of the recording when played back in iTunes.
Has anyone else heard of mp3's doing this in iTunes?
Is there a solution?
Thanks in advance,
PB
PowerMac G5, 1.8Ghz Mac OS X (10.4.6)

Do the original AIFF files sound OK at the same portion in the audio?
Try turning off "Sound Check" in iTunes and playing back the suspect MP3. (careful, parts may come through much LOUDER than you expect).

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