Being in a bad flare definitely can make a difference. My first scope was horrible. I also woke up screaming in pain half way through. In recovery, they told me my colon was spasming so badly, they couldn't get all the way around and sent me for barium x-rays. After that, I started warning the nurse and anesthesiologist ahead of time. You can also request a pediatric scope, which is smaller and less invasive. Of course, they'll probably already be doing this for your son, but I ask for it, too, since I'm a petite female.
Every doc/facility does thing a little differently, I guess. My scope two years ago, they had me count backwards from 100 and I don't think I got beyond 98. I was totally out and remembered nothing. I just had a scope on Monday. This time, I must have been in and out. I don't remember the start of the procedure, but I did wake up during it and watched the progress on the monitor, although I must have been pretty hazy. I'm also a little fuzzy on the recovery period. Made sure my husband was there when the doc came in to talk about the results, because I was afraid I wouldn't remember everything. The lighter sedation was nice in that I only had to sleep it off for a couple of hours. On the heavier sedation, I'm pretty much snoozing the rest of the day. I've never had nausea afterwards.