I take enzymes with meals and snacks. When they were first prescribed, the doctor had me start on low dosage. I took one Creon 10 with breakfast and lunch, and two Creon 10 with dinner. I continued to have the problem you described, just not as bad as before starting taking Creon. Another of my doctors reviewed the medications and my diet, and suggested I increase the dosage. I now take at least two Creon 10's with breakfast and lunch, and three with dinner. I take one Creon 10 with snacks when I have them. After increasing the enzymes, and getting my blood glucose under control, my weight was stable, I digest food normally and have normal bathroom breaks. I have learned how many enzymes to take based on what I'm eating.
Maybe your Father can speak with his doctor about possibly increasing the amount of enzymes taken, or trying a different one to see if it helps. It can be frustrating because it's mostly trial and error until you find what works for you.
Hope your Father sees some improvement soon.