I had a look at your files (e.g. for 0.4mm) and I noticed the following:
1. You are exciting the structure with ports, and thus you do not use the eigenmode solve as you say in the original post. The standard way to get the dispersion diagram is with the eigenmode solver (i.e. without excitation). If you excite your structure you need to do quite a few steps. I suggest to use the eigenmode solver as this will save you a lot of time and will keep you away from many potential error sources.
2. You apply periodic boundaries along the y-direction but from my understanding (after having a quick look at the paper) the structure in your design should be periodic along the x-direction.
Now, if you follow the above steps, in the boundary setup window, under the phase shift tab you can define a variable for the phase shift along the direction that you applied the periodicity (e.g. kx for the x- dir). Enter an arbitrary value to start with. Next, select he eigenmode solver and hit the param. Sweep tab. Define a new sequence and use kx for the parameter sweep. Enter start/stop values for kx (0-180 deg) and the number of points inbetween. On the right hand side of the window monitor the frequency of the modes you are interested in. Finally, click start. This will generate automatically the dispersion diagram under the folder" tables". Then you can easily get the graph you want by normalizing the axis.
Hope this helps....