IPhone – Encrypted iphone backup file has 16gb, but cannot see any files on in

I don't have a great answer - but this is fairly serious so I'm going to start an answer and hope someone else edits or answers if they can spot something I haven't.

On the computer, the only "red flag" would be if you wiped the phone of all content and settings, named it exactly the same name as it was before (which could be iPhone) and then backed up again and overwrote the backup with the actual data. iTunes tries hard to prevent this and spawn off a date-protected backup when it detects this, but I've seen this check fail and people lose backups from time to time. The remedy here is to restore the PC from a backup that has whatever MobileSync folder is the most recent.

On iCloud - you also shouldn't be able to overwrite a "full" backup with an empty one. Also, iCloud explicitly keeps several versions of the backups going back in roughly day intervals. It also normally stores backups for different devices without collisions or overwriting another backup.

The good news on iCloud is you can always get help from Apple at http://www.apple.com/support/icloud/ and from retail stores. New devices or ones covered by Apple Care also have phone or web support in most countries. All new Apple products have a 90 day window of set up help. Hopefully one of these can step in and assist. Not only does Apple get a data point where their tools let you down (and exactly what circumstances this happened) - they also see many people in this situation and will hopefully waste a minimum of your time getting this sorted.

I don't know if this will work or not, but you could try this: Firstly, delete all backups from iTunes. Quit iTunes. Then locate the iTunes backup folder /Backup and delete that. Then copy your backup to that location. Open iTunes and see if the backup is there again. If not, delete the backup location again. Make a new backup. Then replace the backup file from the one in your external drive.
If this doesn't work and no other suggestions work you might want to consider checking the apple forums/support website if someone has asked a similar question. If not, maybe ask there as well.
You could also try taking your iPhone and the back-up in to an Apple Store if you have AppleCare. Not sure if they would help you or not if you don't have AppleCare.