The simple answer might be that the polarity of the X and Y windings are different from each other. The polarity depends on the actual construction of the transformer for either WYE or delta configurations. If these windings are both load only secondaries it would make no differnce if the...
Unless you know exactly what loads are connected to each phase at any given moment and/or what loads may be wired as single phase or multi-phase then you have no way of knowing what the loads should be at the moment you happen to measure. Remember, many items regularly cycle such as fans...
