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MySQL server on Ubuntu fails to start after changes made to my.cnf in Windows

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http://unix.stackexchange.com – I have MySQL 5.5 running on Ubuntu Server 12.10. When I run /etc/init.d/mysql restart, I get the following: mysql start/running, process 2754 However, when I open /etc/mysql/my.cnf in Windows via a Samba share and save the file without any changes, I get the following when running the exact same command, /etc/init.d/mysql restart: start: Job failed to start What is causing the mysql from restarting? How can I make edits in windows without breaking my config file? (HowTos)