I don't think you have to escape the --init-file
parameter:
"C:\Program Files\MySQL\MySQL Server 5.6\bin\mysqld.exe" --defaults-file="C:\\Program Files\\MySQL\\MySQL Server 5.6\\my.ini" --init-file=C:\\mysql-init.txt
Should be:
"C:\Program Files\MySQL\MySQL Server 5.6\bin\mysqld.exe" --defaults-file="C:\\Program Files\\MySQL\\MySQL Server 5.6\\my.ini" --init-file=C:\mysql-init.txt