Divalent cation binding to calmodulin
The change in gel migration distance is due to the conformational changes due to the binding of the ion, and have nothing (detectable) to do with the ionic radius of the ion. 

The left image shows calmodulin with no ligand bound, and the right image shows it with calcium and peptide bound to it. 




As you can clearly see, the unbound calmodulin is significantly thinner, and therefore can migrate faster through the gel. The change in charge on the protein due to cation binding in native PAGE may also affect the result. 

Since the calmodulin conformational change is enhanced by both a peptide and calcium cations, as well as its phosphorylation state, it would be reasonable to investigate the contributions of these factors to your result. Reading the original paper again to see what you missed the first time may also be helpful.