Rectified current transformer output is asymmetric
Bad assumptions 


It is not saturated.   It is poorly driven by a dual switch so that the currents are unequal. Show your drive details or else double the Vgs.
A current transformer never saturate from excess current, rather only excess voltage where the typical threshold is -10% inductance
The rated voltage is 1V out using max current input of 35A for \$R_T=5.7\Omega\$.  


instead you used 40 Ohm Load with sense Voltage on 1K+0.1uF AC coupled, which although not significantly different as you indicated , has exceed the Tesla or weber/m of 1Vsec. /35A.pri.

The fundamental reason of asymmetry is due to your rectifier source not being symmetrical with 2 identical FETs yet different Vgs voltages (apparently) resulting in different RdsOn and compared to 40 Ohms transformed down to primary side presented a significant “Kirchhoff resistance” of I*RdsOn drop in the high side FET.
You assumed we know where your Nodes captured are located
You assumed you had a symmetrical linear circuit