I would suggest that you convert your MP3 file to AIFF before using in iMovie.
You can easily create an AIFF version in iTunes.
In iTunes/Preferences go to the General Tab and click on the Import Settings button.
Choose IMPORT USING... AIFF ENCODER
(Remember what the setting was before you changed it, so you can go back later and change it back)
Now, right-click on your music track in iTunes. You will see a popup menu. Choose "Create AIFF version".
Use this AIFF version in iMovie.
If that still does not help, I suggest trashing your preference files as explained here.