Not sure...but my first two AG batches were definitely "different". My first AG was a Pale Ale and everything besides grains remained the same as my extract batch. However, the AG batch had very slow and steady fermentation which lasted well over 10 days, versus my extract batch which only took 7 days to ferment. My second AG was a wheat...again almost exactly the same as my extract batch, but just a bit more wheat compared to the 60/40 wheat/barley extract I had used previously. This AG batch had some violent fermentation and had a pretty big blowoff, while my extract batch was just very steady...the same as all of my other extract batches.
So I don't really have a good answer to your question I guess...only that I have noticed the difference in fermentation between extract and AG. Not that this is a bad thing...just drank a sixer of my first AG pale ale and it was FANTASTIC. And I took a sample of my wheat beer last night...it too was amazing...so I think fermentation was very healthy.