So here are the facts...
Recently produced 3GSs require a tethered JB. It means each time the phone is rebooted, it must be connected to a PC/Mac and the Blackra1n app needs to be run. Once it is run and boots up, the phone works like it should in the state it was when you rebooted.
That doesn't mean you lose your JB or UL. It only means it needs to be connected to a PC and use BR1 to get past the bootup sequence each time.
Check the serial # of the phone under Settings | General | About. If the 4th and 5th digit of the serial is "40" or higher, then you got a phone with the new iBoot and will require this each time its rebooted, unless/until someone comes up with a way to hack this in the future. And this applies if you use BR1 or PwnageTool/custom IPSW to JB. No tools exist currently to get around this.