Different runs of feature selection algorithm giving different set of selected feature. How to choose the best set among them?
You can set a seed or a random state for the splitting process. This helps in generating a fixed random number everytime, which helps you get the same data everytime you do the CV split.

This can be done by set_seed(...) in R, and adding the random_state = ... in relevant functions parameters in Python. So, please add the relevant parameter for Matlab, and your CV would do good.