To test SQLYog and run it through its paces, I tested it against an employees sample database running locally on a development laptop with Windows 8.1 Professional and MySQL version 5.6.

Hate to "me too" but also having this issue against mysql 5.6 on redhat. Putty works fine and other programs that usually connect to mysql work fine too. Note: worked fine on older version of SQLyog - ...

Open SqlYog and enter the settings as in the image remember to put in correct password and username for the remote server the hostname would remain localhost only. Click on connect and you can now ...