Despite the fact that Toroid A has a higher gain in this plot, toroid B actually has a slightly larger peak signal coming out of the integrator. (see Comparing Toroid A and B in spice) The droop due to Toroid B's shorter L/R time (it has a smaller self inductance than toroid A) significantly reduces the signal before it gets digitized. This droop will cause any jitter in the integrator trigger time to be translated into a jitter in the output voltage.

Toroid Slope Offset ------ -------------- ---------------- A 43.04 +/- 0.04 -0.115 +/- 0.002 B 36.41 +/- 0.07 -0.121 +/- 0.003The offset is caused by small DC offsets in the op-amps in the integrator board.