I have the same problem here.
Got a 3GS with 3.1.2, JB with blackrain and it worked great.
Dummily enough I went to cydia and installed OpenSSH as well as iReboot (I think thats the name, just an app to reboot the phone).
Decided to restart it.
So usb/itunes screen came up, fired blackrain to make it boot and geohot's pic came up for a long time and nothing happened, then it rebooted by itself and went back into the usb/itunes screen.
Tried several times booting it through blackrain but same thing happends.
Tried restoring 3.1.2 from itunes but it doesnt let me, since it tries to verify it with apple, my SHSH on cydia are for 3.1.3 unfortunately.
Tried a custom 3.1.2 restore but it gets stuck on the preparing the iphone for restore screen, then it times out and throws an error.
I dont wanna let itunes upgrade it to 3.1.3.
Model: MC132
Baseband: 05.11.07
Bootloader: 6.4
Firmware: 3.1.2
Hope someone can help on this issue, I cant think of anything else
Had to put my sim back on a Windows mobile, but I am missing my iphone already