"but it seems that it does not work properly"
It does exactly what the save documentation states for that option: "If a variable already exists in a MAT-file, then save overwrites it with the value in the workspace." The problem is not that the option does not work, the problem is that the option is very badly named and some users do not read the documentation. It should be called "replace", or "overwrite", or something similar.
To append new data to the end of a variable in a .mat file you will have to load the variable, append the new data, and then save the variable again. Or use matfile.
