Your filter input impedance is the problem. That is much lower than the 100 ohm R load, such that peak excursions in the PWM are clipped and the midpoints have shifted as a result.
You need to define both the s11 and s21 response specs or the input Return Loss and transmission loss from loading and also the output impedance of your transformed RdsOn Bridges. Then and only then can you design a filter to meet your specs.
Consider the impedances at both line and switching frequency in this operation.