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In what format is your source audio?
Nasty. As Steve said: What kind of sources do you use? Sounds like some MPEG-derivative with multiplexed streams, so AE wastes a lot of time on decoding it in the first place...
quicktime 7.6 update was probably a bad decision.
use the little all-in-1der "mpeg streamclip" for conforming (or demuxing/extracting) all your audio (video formats are possible as well) to AIFF 48khz 16 bit or WAV,
Both work well.