If it is really chronic, it can be a sign of a lot of things. One of them is allergies. Usually the first thing you do with chronic allergies is change the food to a food with little to no ingredients that are the same as the old food and try it for about 3 months and see if the stools get better.
Maybe I am wrong, but fibre should not affect the water absorption in the colon, it would just affect the frequency of 'dumps' and the quantity of them. If the loose stool is really because of the cookies, is the stool solid on days where the doggy doesn't get any? (He could also be allergic to the cookies...)