How is this a quantum effect? Clocks can be noisy, so if your board isn't designed to keep everything isolated properly, you'll pick up noise all over the place. It's an electromagnetic effect, sure, but a quantum effect?
So, I believe this would be an "effect on the quantum level," even if it can be understood through the lens of more traditional electromagnetic physics as well.
EDIT: Not trying to diminish the OPs impressive feat of debugging though. Hardware errors can be beastly to diagnose. When wire-wrapping an 8086 computer, I used a spool of wire with occasional (random) breaks that would intermittently open. Worst. Bugs. Ever.