Whelp... turns out that I stuffed up the pinout and need to re-route and re-spin so that the Timer/Counter channels and so on are hooked up in the correct places. This thing was a pain to route in the first place -- so much fun to do it again!

Since this project uses three different timer/counter peripheral functions (PWM, timer interrupts, and encoder input), I need to be pretty careful about how I use the peripherals.