Things you might want to try first:
-Power down/power up the phone *
-Hard reboot the phone (hold home and sleep for several seconds until the screen turns black) *
-check our services, make sure that "apple mobile device" service is "started" and "automatic".
-make sure the iTunesHelper process is not running. It causes iTunes to start whenever your phone is plugged in, and possibly try to start restoring it a3utomatically.
*doubt these would work, and might be due to this:
Hey folks - bought my 3gs the other day. Latest firmware, iboot, the works.
Ran blackra1n and like everyone else, it was stuck on the 'connect to itunes' screen. I tried pwnage, rc2, everytime I was stuck I had to restore via itunes to factory settings just to get it back to working.
Ran blackrain again. Got the itunes pic on the phone. BUT...With the phone still connected via usb, open and run Blackra1n again (2nd time) and it reboots and voila! JB'd.
Every time the phone cycles off/on, you're going to get that connect to itunes image on the phone, you have to run blackrain.
I hope this helps. I spent HOURS trying to figure this damn thing out and no one was helpful to me. I hope this helps you.
Now, that doesn't sound too encouraging, since it means you can't reboot your phone whenever you want, but it might help you get it up and running again.
Just in case, it might make a difference if you're running blackra1n RC1, RC2, or RC3. Try using RC3. You might also want to see the guy's blog:
http://iphonejtag.blogspot.com/Not sure if any of this directly addresses your problem, but some of it might help.