You may not be heating the milk enough in the first step - cornstarch is activated at around 200°F (95°C), which means it needs to get to 200°F to start thickening a liquid. It is also possible to overmix the starch and break up the structure, but you do really need to whisk excessively for this to happen. Only use a whisk, never an electric mixer. Once your pudding has thickened, stop whisking it and move on with the recipe.