are you sure it is the exact same shot? there are many things that could be happening, most likely it is your error.
if you want to really see if it works, try shooting in M mode at your widest aperture and exposing correctly with shutter speed and matrix metering. auto ISO will try to expose the shot correctly, so if you have the correct exposure from aperture and shutter speed, it should be adjusting to around ISO200. Then the TTL should fire only minimally as you are on matrix metering and already have a correct exposure.
that said, i am never happy with auto ISO with on camera flash, it tends to give less than ideal results. I exposure for the shot and usually need scene/shadow detail, so might manually crank the ISO to get a scene 1-2 stops under exposed, then add flash as needed.
don't blame your camera if you always shoot it on auto, that is why it has manual settings.
Before posting this, I did a poor mans test, hand holding the camera, and aiming at same shots with 2 diff settings. It was easy to see that the P mode was always going to my max setting of 3200.
I almost always shoot M but rarely do flash pics so that's where my lesser understanding came in to play. I'm not an M mode prude tho... not every pic needs to be taken in hopes its the one to knock Ansel Adams off the top list. Sometimes I just want to snap fast and good pics of the family holiday dinner so I have no problem going auto there. I'm sure Steven Spielberg doesnt use a $500,000 movie camera to shoot home videos. :-)
Plus.. I found info on the Nikon site that seems to back up my thoughts?
I'll do another test tonight... same shots, different settings. Bonus is... I bought my wife a 3100 for Christmas and I'll be able to try the SB600 on her camera also (which, if I am reading the nikon site correctly, should auto adjust the ISO)
Thanks for your input and suggestions!!!