so will my unconfirmed still confirm ?
There's no guarantee. All you can do is join the rest of us and wait... and wait... and wait. I have two unconfirmed payouts totaling around 2.25 BTC; both flushed from the blockchain.info ledger. I've written them off as a loss at this point, but we shall see.
It's good that the op is making changes to reduce these problems in the future but those who have potentially lost coins are probably shit out of luck.
@wp.cointemp2, what about the payout double spends? Are those fixed?