Kerim,
But your 3-winding transformer:
- is really just a 2-winding transformer but with a center-tapped primary (does that matter?);
- is "perfect", with no leakage inductance.
If the leakage inductance is responsible for the transformer's low-pass filtering, the 3-winding transformer lacks any.? What did you do to it when tweaking it to act as an LPF?? You did not leave your tweaks on the schematic, right?
Andy