Wow, this is being pretty crazy...it's like nothing on your machine will work the way it's supposed to.

Anyway, since we know the file definitely exists, try:
Code:
cd /etc/init.d
sudo update-rc.d wifi-fix.sh defaults
Maybe that will help because you won't be giving it the full path to the file. It seems to me that there's some bug with update-rc.d that's making it interpret the command-line arguments incorrectly, which is why it's repeating '/etc/init.d.'

If it still doesn't work, you can update the init scripts by default--basically you just have to symlink some things together, which is all that update-rc.d does--but hopefully that won't be necessary, as it's tedious.

And no, unfortunately there's no GUI that I know of for writing boot scripts--although it would be a nice feature that would be trivially easy to write, I think. Gnome has a GUI at System>Preferences>Sessions to run commands when you log into Gnome, which we could use to call the wifi-fix.sh script, but it would be a lot cleaner and better to have init deal with it.