Hisses and pops in both Final Cuts

Hey guys,
I've been having some weird problems. Since I upgraded from Final Cut Express to Final Cut Pro, all my video (both rendered and exported to various formats) have hisses and pops in the audio. The problem now also occurs in Express. Did an audio codec get damaged or something?
By the way, I'm simply a beginner. I'm working as an intern, and haven't worked with video all too much.
Can anyone help me?

The MP3 thing does help a lot. Fixed some other files by converting the audio up front. But in many cases the problem still continues to exist, even after re-installing. For example when importing video files of different formats. when rendered and played, the sound completely disappears for a fraction of a second every couple of seconds.

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