I sent 1.5B Pennies from one wallet to my PFQiBugkv6jywNy89Xo5FH7anE8qdMAffP address but they never showed up in the wallet after >500 confirmations

Sent them in small transactions of ~5M each.
Wallet is in sync.
Redownloaded the whole chain.
Did a repairwallet on old and new wallet.
0.9.6 wallet.
Transaction ID's show up in block explorer, but no Pennies...
Out of options

Did you try "-rescan" from the command line and check the log? Also check to see if the # of transactions listed on the main pane matches the number in the ledger. I have had a similar problem in doubloons, where the client clearly counts and tries to add the transaction but it doesn't show up in the balance/log.