Unfortunately Final Cut is still pretty finicky when it comes to Audio formats. I recommend getting all audio into the AIFF format (48Khz is typical) before pulling it into Final Cut. This is where Quicktime Pro can be your best friend! Quicktime Pro has many export options that can save the day for this exact problem.
One extra problem with itunes files is their proprietary coding system. This is usually very unfriendly and many sytems can't even convert it out into something usable. If your using the MP3 format then getting to AIFF will be easier.
The clicking your hearing on the audio is usually a sample rate mismatch. Meaning your audio is running at 48khz but your edit window is set for 44khz. Another problem could have been on the import. Again first get it to an AIFF then import to Final Cut! You'll be happy you did!
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