Is your upgraded client "up to date"?
Your balance will show as zero if it has ended up re-loading the blockchain until it gets to the point when you "acquired the coins" (i.e. it might just "come good" if you wait).
Also - "don't panic" and make sure that your backups are kept intact.
(and yes - use blockchain.info to check the balances of individual addresses to verify whether or not any coins have *moved*)