Oh, so it' still Pwnage tool. It's been awhile since I've jailbreaked. Like last year at 3.X.X something. I am not planning to jailbreak again until 4.0.0 comes out later this year.
ok here is how you can ailbreak with blackra1n when you have 3.1.3
download the 3.1.2 .ipsw file
then open itunes and shift+click the restore button
find your .ipsw file and install it
you cant jailbreak 3.1.3 with blackra1n unless you rollback the software to 3.1.2 or under