I'm not sure, but my guess would be that your nerves are playing a big part in what your small intestine and sphincter muscles are doing throughout the day. My best bowel movement of the day is always a morning one, and I've always assumed that the reason for that was that I was sleeping for hours prior to that bowel movement, so my body was calm and did what it needed to do. After I wake up and start my day - I'm moving around, my nerves are awake, I'm eating, etc. etc. All of this gives my body less of a chance to get the bowel movement formed, not to mention gravity working against me. I'm sure there is a much more scientific explanation that someone after me will articulate. Just know that you're not alone! I have the same trouble when I'm in a flare. I never really thought to get an official answer from the doc though. Best of luck to you, and like I said - I'm sure someone will be along soon with a more researched answer!
26f, dx'd CD July '05 after 6 fistula/abscess surgeries
Remicade only, every 16 weeks.
Digestive enzymes, and probiotics.
Doing pretty darn good, all things considered.
"Our greatest fear is not that we are inadequate, but that we are powerful beyond measure."