I don't know what could be wrong at this point.

However, if you use the Classic GUI and set the mode to 'Expert Mode' in the Preferences, then you can see the actual balance in each bitcoin address in your system by then selecting the 'Receive' tab on the main screen. You can compare these balances by using either btcbalance.net, or by checking each address using blockchain.info by adding the address to the end of this URL, like this:

http://blockchain.info/address/1GcKb752rgkeYC2w72dgpoCUQBpEmHAkYZ

Otherwise, there's no way to figure out the problem just by looking at wallet ledger entries.