If you're talking about a heat mat (heat pad, heat tape, UTH, etc), then it's functioning exactly how it should be functioning. They're meant to raise the temperature of what they're in contact with and not meant to raise the temperature of the entire enclosure much at all. I'd put money on the glass where the heater is actually being way too hot for your BP. The picture shown above is how to properly mount a heat mat (i.e., with a thermostat) to make sure that the surface your snake is resting on doesn't become too hot and burn your snake.
How are you measuring your temperatures? An infrared heat gun (you don't have to spend more than $20-$30 on one) is going to be your best bet. Here's one I recommend: Etekcity Lasergrip 1080 (ETC 8550)
Do you have a thermostat at all? If not, this is probably the most important piece of equipment you can buy for your snake to keep it safely. Here's the brand I recommend: Spyder Robotics Herpstat