@harilalp I moved your post to this older topic dealing with this issue.
Make sure you don't have any other program using MFF files (eg. EEGLAB or FieldTrip) running in the same Matlab session. You'd need to close Matlab before switching between different programs using different versions of the mff IO library.
Note that could reach similar issues by using the function clear in your personal scripts.
Never call the function clear after Brainstorm has been started.
I also pushed a commit that stops asking continuously to update the mff plugin.