The red flag thing with IBS comes from a study where they took a whole bunch of IBSers and a whole bunch of people with other GI illnesses including GERD and inflammatory bowel diseases and maybe a few others.They got information about symptoms and timing of symptoms and stuff like that.What they found is healthy people rarely get woken up in the middle of sleep with diarrhea or abdominal pain.People with GERD commonly get woken up with pain and I know that some of the IBD's (especially microscopic colitis which isn't one of the main two but runs that way) can cause issues during the night.IBSers were more likely to wake up in the middle of sleep with problems than healthy controls, but less often than you see in other diseases.Red flag does NOT mean you can't have IBS it must be something else. Red flag means that symptom may be more common in another disorder and you may need a few more tests before they decide it is just IBS. If you have diarrhea several times a night on any sort of regular basis you probably need a colonoscopy with biopsies. If you have abdominal pain waking you at nigh (especially higher in the abdomen) you probably need to be screened for GERD. Sometimes these symptoms happen in IBSers but since they also are more common in something else you may need to check for those things before just saying they are a part of your IBS.The colon normally "goes to sleep" when you do. That is to say it is a lot less active during sleep than it is during the day.It typically has a burst of activity around getting up time. Why that bothers you when you get up with an alarm at a specific time compared to when you get up naturally may have to do with how the alarm wake up stresses you or that it doesn't allow you to get up at the point in your sleep cycle where it would be natural for you to wake up.IBSers tend to have symptoms when the colon is more active. It cycles through periods of high activity during the day. It will do that after you eat (so why it can go off several hours after you got up) and around the time you get up, but it is not limited to just that, but those are common times for IBSers to have issues.