Line to phase voltage with harmonics
Remember that there are voltage harmonics, because of the current harmonics. I mean, that voltage harmonics are "generated" by current harmonics. So, if the three lines impedances are not exactly the same, then the voltage drop generated by the 3rd harmonic current in each line will be different. 

Have you tried to measure currents instead of voltages?
You may go to phase voltage from line current (analizing the voltage drop)

*If I wasn´t clear I can write it in spanish (Im from Argentina and my eglish isn´t good enough sometimes)