Went back this afternoon and exposed this run. I definitely left the stone too low (about 300 from finish) but have now brought it up near the top and left uncovered.
But it is definitely picking up some water, I could see it seeping in the side of the trench.
This run is parallel to boundary, runs downhill with the garden but yes the water is coming perpendicular off the neighbouring garden.
Most of the garden is ok to work off with the track mats but the bottom corner is just soup. There's no drain on this last bit so I dug a trench down to the other drain so the standing water could run off - it was pouring through from the garden next door.