There are three counter/timers in the atmega328 (more on the chip used in the Mega) and from your description, it appears that the Auduino code uses one or more of them. Each counter/timer controls two of the PWM pins. When you are using a counter/timer for something else, you can't use its associated PWM pins.
I suggest you temporarily modify setBacklight() to write to just one PWM pin, and thereby establish which PWM pin(s) cause the problem. Then try switching those to the spare PWM pins, assuming you have some.
Alternatively, look at the Auduino code to see which counter/timer(s) it is using, then you can work out which PWM pins are available.