Hi Gavus, welcome to geekhack. I haven't looked over your schematic in detail, but I did notice that you have 2 of the LEDs on pins without hardware PWM. LED_A is on PC7, so that's fine. You can, of course, use software PWM, but moving the others to something like PB5, PB6, PD6 or PD7 would put them on the hardware PWM pins (at least as far as I remember). I'll take a closer look when I get a chance. I'd love to see (I'm sure others will also) what your overall design is, if you have any drawings or anything.