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Presumed inductance values have been correctly measured, reversed winding polarity is the only way to get a lower inductance in the second configuration. The numbers indicate however a relative low coupling (about 0.63) of both windings. Can you explain the core configuration (dimensions, material, possible air gaps)?In the parallel configuration, the winding polarity is such that they are bucking each other (look at the flux direction of each).
Reverse the polarity to one of the windings.
Hi FVM,You didn't mention yet that inductance was apparently measured with secondary winding in place. In this case, I won't expect a meaningful measurement at 100 kHz, too close to secondary winding SRF. Main and leakage inductance can be better measured at 1 kHz. Another problem is the magnitude dependency of ferrous core permeability.