Teensy 3.1 PWM, TIP31C, and LED strips
... emitter is wired to ground, base straight to a PWM pin ...


VBE(sat) of the TIP31C is 1.8V. Every time the output goes high, the MCU has to burn up the voltage difference between the supply voltage and VBE internally. This is not good for the chip. Put a resistor on the base so that there is an additional external component to drop this voltage over instead.