Wallets created with this version of bitcoin will use 33-byte 'compressed' public keys instead of 65-byte public keys, resulting in smaller transactions and less traffic on the bitcoin network. The shorter keys are already supported by the network but wallet.dat files containing short keys are not compatible with earlier versions of Bitcoin-Qt/bitcoind.
Use a recent wallet backup.
Also, as a general piece of advice, please don't use unstable (beta, release candidate,...) software for mission-critical tasks.
While I do have bitcoind 60003 up and running here, it's only a test server with a total of 1 BTC to play with.
When the version 6 client gets the final
status it's the authors way of telling you that it should be safe for production environment.