I had a very similar issue to this when testing a restored backup of a mysql and associated php system. No matter what configuration settings I added on mysql it was not making any difference. After troubleshooting the issue for some time I noticed in the mysql logs that the mysql config files were being largely ignored by mysql. The reason was due to the file permissions being too open which was due to the fact my zip backup and restore process was losing all file permissions. I modified my backup and restore scripts to use tar instead and then everything worked as it should.
In summary, check the file permissions on your mysql config files are correct. Hope this helps someone.