you are using the wrong value tone pot...by the time you are at 3 on a 500k you probably have similar resistance to a 250k at 10.
just a thought,
if you are using that schematic, note that in series mode the bridge vol is unused, so you could use this p/p pot as the bridge volume and then you will have a 250k pot available for the tone control.. you may hear a slightly brighter tone due to the reduced loading of the 500k over the 250k and a loss in sensitivity to knob movement on bridge vol in parallel mode.. (since its now 500k vs 250k)