Why Homemade Pudding Fails to Thicken

I am making homemade pudding every week for my mother in law who is on a solid restricted diet. My problem is I have about a 50/50 chance of it thickening properly. All recipes use cornstarch and it is my understanding the pudding temperature should not go above 180F. I use my trusty instant read thermometer yet I still have failure after failure. I give up. What would be wrong with using ap flour as a substitution? Still on the pudding note - When a recipe calls for whole milk could I substitute 1% or 2% milk and replace a portion with heavy (35% cream) or half and half? I almost always have creams but seldom whole milk. And yet another pudding question - I am attempting to add more protein in her diet and it seems most of the time if I add an extra egg it causes the pudding to thin again. Is this in my imagination?