If you're near an Apple Store it would be interesting to hear what they have to say about your problem; they may have a utility that will give them answers that we mere mortals can't get at.
We don't have an Apple store, but there is an Apple authorized dealer just a few blocks from where I live with a pretty good service department. I may drop in and ask the service guy next time I'm over there.
Meanwhile I found a discussion of the problem on discussions.apple.com. One person said that simply syncing the phone isn't enough to restore the missing storage, and suggested doing a backup followed by a restore. I tried this to no avail. However, I downloaded the free iBackupBot utility which can be used to examine the files in the backup. Interestingly, the total size of the backup files is only about 650MB. So, there's no excess consumption in the backup. So, it looks like the next step will be to do a factory reset followed by a restore from the last backup. I'll let you know what happens.
