Have you tried to force the mesh symmetric and then compare with symmetry BCs?
make sure the dipole is located at the Ey position in the Yee cell. You can zoom in the mesh and make sure it is there.
You can also use a monitor, and compare the monitor xy data with symmetry BCs and without, as well as force the mesh symmetric.
The change of the result is mainly due to the mesh change.
If you want to know more about Yee mesh and FDTD, please find a FDTD book, or some online resources.
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