Here's a solution that worked for me, even after I updated to the stock 3.1.3 software.
Open redsn0w & use 3.1.2
Wait for redsn0w to start the restore.
Once the iPhone turns white, unplug it and close redsn0w
Open iTunes, and flash your custom 3.1.3 ipsw using shift + click or alt + click.
Open redsn0w & use 3.1.2
Wait for redsn0w to start the restore.
Once the iPhone turns white, unplug it and close redsn0w
Open iTunes, and flash your custom 3.1.3 ipsw using shift + click or alt + click.