Unfortunately, this script does not preserve permissions and files will lose their executable state (script version 0.9, on Unix based systems). Fixed in 0.9.1
Version 0.9.1 is identical to 0.9.0 on http://www.vim.org/scripts/script.php?script_id=3641 . Script upload error?
Ooops. Guess I uploaded the wrong one. I fixed it. Sorry it took so long, I had no idea.