You are using deep groundwater and logging at the bottom of the soil columns, which mean water should only move downwards. I think NO3-Matrix-Leak should never be negative in such a system, and certainly not like the three big events.
My best guess is that the advection-dispersion equation fails to solve correctly, and Daisy give negative leaching to maintain mass balance.
I suggest trying the 2D solver, which is slower, but uses an entirely different solution to the transport equations. It is the "Movement rectangle" stuff below:
;; soil column definition
(defcolumn ES_profile default
;(Surface (EpFactor 0.9))
(Soil
(MaxRootingDepth 120 [cm])
(horizons
( -30 [cm] A_soil_20_sample1)
( -90 [cm] dummy_soil_20_sample1)
( -120 [cm] B_soil_20_sample1)
))
(Groundwater deep)
;; This switches to the 2D solver:
(Movement rectangle
(Geometry (xplus 1 [cm])
(zplus -2.5 -5 -10 -20 -30 -40 -50 -60 -70 -80 -90 -100 -110 -120)))
;;
(Groundwater lysimeter)
(Chemistry original
(combine (N (reaction nitrification
(denitrification
(water_factor (0.721 0.000) (0.978 0.110) (1.0 1.0)))))))
)