In reply to Andrew Konstantaras.

Hi Andrew!
It looks like it is a kext cache issue: the changes were applied, but OS X is still loading the cached version of Soundflower, which has the old plist.
The Apple-sanctioned way to trigger a cache reset is to touch /System/Library/Extensions (plus /Library/Extensions with El Capitan, I think), then reboot:

sudo touch /System/Library/Extensions /Library/Extensions

If it doesn't work, you can't try the hard way:
sudo kextcache -system-prelinked-kernel
sudo kextcache -system-caches

And then reboot.