I had the exact same question after I generated this block
http://blockexplorer.com/b/129556. I think I managed to work it out, but I don't know what I did is necessary or not. I found my default key via bitcointools. Then I created a new account containing that key:
bitcoind 1CnoM8QYx3Fuijuo4MRLgK5e5DvhsTqzcY mygen
Then, listaccounts showed the new account as well as the unnamed account containing the balance. Then I sent the balance to my address (transaction here:
http://blockexplorer.com/t/661USs4LPM):
bitcoind sendtoaddress 1CnoM8QYx3Fuijuo4MRLgK5e5DvhsTqzcY 50.03
Now listreceivedbyaccount returns the correct amount in the new account:
[
{
"account" : "mygen",
"label" : "mygen",
"amount" : 50.03000000,
"confirmations" : 4
}
]
I hope this helps. I would be grateful if someone more knowledgeable could fill in some details.