FWIW, The stand alone version of Melodyne Editor 2.1.2 does just as good a job of messing up the timing as the version you use inside your DAW. The rendered results ebb and flow before and after the original wave file.
I was not aware that Melodyne did not work correctly in the first 4 versions of SONAR X3.
I just know that Melodyne Editor has some general problems and that if you make the effort to learn how to use it you'll probably be able to figure out what they are.
Launch Melodyne Editor 2.1.2
Open file.
Center Pitch.
Save as.
Compare timing with original.