Got me, at this point. By manually manipulating transactions I've got some wallets with wierd balance info.  It doesn't sound like you've been (intentionally) doing anything like that.

Worst case if you just have to know, create a new wallet somewhere else and send it the coins.  It won't solve this mystery but you will be able to see where your coins are. Just about every exchange handles LTC if you want to use an exchange wallet for this you can pick one with more moderate fees.