You have to give every single argument as one element of a list:
z = ['MP4Box', '-cat', 'test_0.mp4', '-cat', 'test_1.mp4', '-cat', 'test_2.mp4', '-new', 'test_012d.mp4']
subprocess.Popen(z,shell=False)
This is normally what you want to do, because you don't need to escape especial characters of the shell in filenames.