Originally Posted by digitalfx
OK, it looks like your OmniFocus file is there, as is the lockfile (which tells another instance of OmniFocus not to edit the file, to avoid conflicts).
1. If you quit OmniFocus, is the OmniFocus.ofocus.lock file still there? If so, delete it and try restarting.
2. With OmniFocus open, what happens if you manually choose Back Up Database... from the File menu? If it opens a dialogue, can you save the backup to your Desktop (or some folder besides the default ~/Documents/OmniFocus Backups folder)?
3. If you can make a backup of your current database, then quit OmniFocus, drag the file(s) and folder(s) in ~/Library/Application Support/OmniFocus/ and the file ~/Library/Prerences/com.omnigroup.OmniFocus.plist to the desktop, restart OmniFocus (which should recreate the default file and preferences), and then choose File > Restore from Backup... and then restore using the file you created in step #2.
Step 3 should essentially result in a new database, without your preferences and Perspectives, followed by replacing that database with the backup. You'll have to re-enter all your preferences, and resync with the iDisk. When you resync, you'll be prompted as to whether to use the local copy or the server copy of the database: if the preceding steps have all worked, and the newly restored database is the one you want, then choose local copy.
Disclaimer: I don't work for the Omni Group, I don't know what goes on under the hood, and I back up religiously. I'm providing these tips to give you a hand until Omni's tech support ninjas can get back to you, so please don't blame me if you lose data! But unless there is some deeper problem with your hardware or software, these steps should produce a working database. If you still have to re-enter all your tasks after each new version, then you might want to get your computer checked out.