If you have OmniFocus on your Mac, sync it up, then force a backup (File > Back up Database). Check the size of that backup you just made. If it's still about 1.2 MB, please email
omnifocus@omnigroup.com so we can figure out what's going on.
If it is smaller, move aside the OmniFocus file on your iDisk. On the Mac, choose File > Revert to Database and choose the backup you just made. Now sync it back up to your iDisk. Now sync it to your iPhone (if it asks whether to use Server or Local, choose Server.)