I've been on CAP for almost 21 months with the exception of a 3-4 weeks break over this past summer. Never had a problem with stool. The worst I've had in these months of CAP was a soft stool 2-3 times a day.
Well, a couple of weeks ago I switched to a different thyroid regiment - I decreased my Synthroid dose and added Armour Thyroid instead (together to match my previous dose of Synthroid). At that time I already had been on Flagyl pulse for 5 days in addition to my 3-abx CAP. I do Flagyl pulses as long as tolerated. When I started new thyroid treatment, I noticed frequent soft stools which was welcome b/c on Flagyl I usually constipate. However, over the past 2 weeks it slowly got worse and today I am having completely liquid stool but without any cramps or pain.