If you have a standard macbook, it's HD is running at 5400rpm which isn't recommended for video. Even if you had a 7200rpm drive, it's recommended to run video (have your scratch disk) on an external HD.
Minimum recommended spec for an ext drive is 7200rpm, firewire.
Also might be worth considering not running any other applications while running FCE and repairing permissions once in a while:
1. HD/Applications/Utilities/Disk Utility
2. Select your mac in the window
3. Click on Repair permissions.
4. Restart your mac once finished.
This may not help your issue but is good practice for maintaining your mac and many people recommend doing this process once new software has been installed or every week or two.