I think you should go a different route where you don't save your variables to .mat files and simply keep the variables in your MATLAB workspace without clearing.
run('script'); % execute your script however you like to
data1 = diff;
run('script'); % execute your script again however you like to
data2 = diff;
run('script'); % execute your script again however you like to
data3 = diff;
plot([data1;data2;data3]');
Or to rename you variable diff (in the script) before running it the second time and third time (e.g. to diff2/diff3)
If you have to store the data in files you could specify an output to the load call
data1 = load('data1.mat')
data2 = load('data2.mat')
data3 = load('data3.mat')
plot([data1.diff;data2.diff;data3.diff]')
