CentOS 6.4, Atomic repo MySQL 5.5.31-16.el6.art, MySQL cookbook version 3.0.0 and 3.0.2.
Ubuntu 12.04 running Percona Server 5.5.31
There is an issue with the Yum installer (possibly other installers as well) creating a default my.cnf file and the MySQL cookbook overwriting with the template as the last step in the recipe.
Generally this would probably not cause many issues HOWEVER one that we came up against was changing the data_dir and log_dir attributes. All changes happen on the default InnoDB files (ibdata and ib_logfile*).
Issues include not setting the grants correctly, not deleting the test database and also causing InnoDB file corruption which stops the service from starting.
I have fixed and tested against my environment but I can't be 100% confident no issues have been introduced against non-RedHat distros. Will add pull request to comments.