Account balances have *no* relation to which coins are available. Coins are always selected from the total pool your bitcoind knows about, accounts are just an accounting tool.
Your total balance (which is the sum of all available coins) will always be positive, and if the client is able to create a transaction, it will be valid (though it could be a double spend, in which case it won't confirm).
In short: just keep your client open and connected, and a wait a bit; the transaction will confirm. The fact that it is slow has nothing to do with account balances in your own client.
How long is "a bit"? The transaction is 11 days old by now. I think I have to fix it somehow - normally, transactions go through after one block for me.
By the way, as you are saying that coins are selected from the total pool, does this mean that accounts will not allow me to control which addresses the money I send is taken from? So I will need to have several wallets to do so?