This probably doesn't help, but your regex works for me when I run it. Can you give more details as to how it's failing for you?

$line = "this is a test [[ this is a test ]
]";
$line =~ s/\[\[[^\]]*\]\s*\]/***FOO***/sg;
print "Line: '$line'\n";
[download]

prints

Line: 'this is a test ***FOO***'
[download]

You also don't need the /m modifier in this case, since you're not using ^ or $ in your regex.