I swapped the old chip for the new one, but it still didn't work. I then rebuilt the first part of the circuit on a breadboard, and it sort-of worked, but both flip flops in the package seemed to flip and flop at the same frequency, which they definitely shouldn't.
Today, I tried adding in a 2k2 resistor between the D and not-Q ports, as well as a 100nF cap from D to ground, a trick I found somewhere online when I originally designed the circuit. This made the circuit work again.
Doing this on the PCB would require me to cut some traces, which would be a lot of trouble, especially on the SMD-based quad suboscillator.
Luckily, when i replaced the 2k2 resistor with a wire, while leaving the cap in place, it still worked :) I soldered two caps onto the pcb as well, and it too worked like it should. I have not tried the board at various frequencies, but for the time being it seems to work fine.
While searching for solutions to my problem, I came across this post named "cd4013 weird shit" - that really sums up my thoughts about this whole problem too...
|The fully populated sub oscillator board. It looks a bit like a bug of sorts, don't you think?|
|A closeup of the 100nF capacitor. Also note the beautiful curved cutouts, I just love the boards OSHPark are able to produce!|