This could have to do with the size and thickness of your bell peppers or possibly the actual temperature of your oven. A lot of ovens run up to 25 degrees too hot or too cool. You can use a small hanging thermometer to test the accuracy of your oven thermostat for future reference. In the meantime, adjust your cooking time as needed. If the peppers are still too firm, cook them longer in 5-minute increments until they are at the desired temperature. If the cheese on the top is getting brown, cover the pan in foil! Another option is pre-baking the pepper for about 10 minutes so they are softened up before assembly.