I have never had any problems working with wav files in FC. I do not work with mp3 files. I always convert them.
I have had issues with audio that was 44K and not 48K.
How are they identical?
Do the frame rates match?
Did the audio exported for mix have a 2-bip?
Does the final mix have a 2-bip? If you aren't doing this I would strongly suggest considering it the the future.
If you are determined to do the reinstall, you can use FCS Remover (free) from Digital Rebellion to remove everything prior to the install. Make sure you have all your serial numbers, etc. espcially if you have upgraded FCS as you will need your original full version serial number in order to do the install.