Well, my achilles didn't bother me for the first 30k or so. But that doesn't mean I was only irritating them in kilometers beyond 30km, just that it took that long to become noticeable.

Maybe you're seeing something similar; at low cadence the problem doesn't become noticeable in the distances you're covering (fewer total pedal strokes?).

Slowing down, resting, healing, changing your cadence... it all might help reduce the irritation, but it probably won't solve the original cause of the problem, which is likely biomechanical (e.g., saddle height)