The X3D exporter seems to ignore the up- and forward-vectors. Attached you find a Blender file with two X3D exports, one of which was done with X-forward and the other with Z-forward. I would expect a difference in the exported file, but there is none (except the embedded file name).
Blender 2.65 64-bit, Win7 64-bit, NVidia GeForce GTX 470
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can confirm this. in my tests this only happens if "Hierarhy" is unchecked.
In this case the global_matrix resulting from the axis_conversion isnt used. will submit a patch for review next