If quitting Final Cut Pro and repairing permissions doesn't fix your Final Cut Pro issues, the next thing to try is throwing away Final Cut Pro's preference files. Every application has at least one preference file, Final Cut Pro has four. In Final Cut Pro versions 1 through 4, throwing away preferences is a pretty common task as they seemed to become corrupt somewhat easily. In Final Cut Pro 5 or 6, the preferences seem far more stable (as is FCP in general), so try the previously listed solutions first before trashing preferences (specifically restarting Final Cut Pro and Repair Permissions).
Saving Favorite Effects When Trashing Preferences
By the way, when the preferences are trashed, you also lose any pre-saved "Favorite" effects stored in the Favorites bin in the Effects tab of the Browser. To protect those effects from permanent deletion, follow the steps below before throwing away the preferences. If you do not care about saving favorites, skip past these next steps.
1. Click on the Effects tab of the Browser.
2. Single-click on the Favorites bin.
3. Press Command/C to copy this bin.
4. Click on the project tab of the Browser (with a current open project).
5. Press Command/V to paste the Favorites bin into the Browser of your current project.
The favorites are now stored as part of the project and will be preserved when you trash the preferences. After you've trashed the preferences, open this project, and copy out the effects from the saved Favorites bin and paste them into the Favorites bin on the Effects tab (which will now be empty). This can be done by double-clicking open the Favorites bin on the Effects tab. Once opened, paste, and the contents of what you copied will now show up back in the Favorites bin.
How To Trash Preferences
1. Quit Final Cut Pro.
2. Double-click open your main hard drive from the Desktop.
3. Navigate to your "Home" folder (this is the "house" icon in the left side of the open window).
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Home icon in OS X 10.4 (Tiger)

Home icon in OS X 10.5 (Leopard)
4. From there, navigate to: Library > Preferences.

5. Locate the file in the Preferences folder: com.apple.finalcutpro.plist
6. Throw this file in the trash.
7. Also in the Preferences folder is a folder called Final Cut Pro User Data. Click into this folder.
8. There may be several sub-folders here, and three individual files. Throw away the three files shown below, but leave the sub-folders alone.

The files are:
Final Cut Pro 6.0 Prefs
Final Cut Pro Obj Cache
Final Cut Pro Prof Cache
When you re-start Final Cut Pro, the preference files are re-built automatically with default settings. You will need to reset the User Preferences, System Settings and Scratch Disks.
Here's a link to an article at kenstone.net for these procedures for earlier versions of Final Cut Pro: Trashing Prefs in FCP 3, FCP 4 and FCP 5: http://www.kenstone.net/fcp_homepage/trashing_fcp_prefs.html
Here's a link to a shareware program called FCP Rescue that backs up, trashes and restores a backup of your preferences. There are different versions for Final Cut Pro 4, 5 and 6: http://fcprescue.andersholck.com/
Note: you must have a good running set of prefs before you can run this app the first time. In fact, the best time to do this is right after you have trashed prefs and have reset them. Now you have a clean, fresh set of preferences to back up.

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