Perhaps you synced with a different wallet and maybe moved the one with xxxx.000 PPC into the folder post-sync. I’d suggest running -rescan and see if that helps. Also, if you know your PPC address you can simply check the balance with a blockexplorer while you wait.
Scenario
Wallet-A is currently in your peercoin directory.
You start the v0.6 client and sync with the network.
Balance shows 0.51999 PPC
You close the client, move Wallet-B into your peercoin directory, and still see 0.51999 PPC balance.
You’re confused because you just moved Wallet-B into the directory and the balance is not 0.51999 PPC.
The issue might be that you didn’t sync with the network while Wallet-B was in your directory but rather while Wallet-A was in your directory.
You can perform a -rescan so that the balance correctly reflects the balance of the addresses held in Wallet-B.
Make sure you keep the backups of you wallet.dat safe!
Export the private keys of the addresses that contain your coins, they will make sure you can always access your coins.
In the debug window do: dumpprivkey <address>
Keep those keys somewhere safe.
You can restart your client without a wallet.dat in your datadir so it’ll create a new one. Then you can import the private keys you just exported in the debug window: importprivkey <priv_key>
Or you can wait for v0.6.1 to be released soon as it’ll have an extra wallet recovery function zapwallettxes which might correctly restore your wallet without having to reimport your keys.