Minimize window with Docky conflicts with Unity
Solution 1:
I tried looking up this problem in other forums but none helped. So I came up with my own alternative method.
1) Change Unity Launcher's position to bottom
That can be done by running the following command in terminal
gsettings set com.canonical.Unity.Launcher launcher-position Bottom
2) Make sure auto-hide is enabled for the unity launcher and set its sensitivity to the lowest
(http://i.imgur.com/snzNQrA.png)
3)Press super key and add random apps to the unity launcher until it line ups with the docky placement.
(http://i.imgur.com/QbJc7Fu.png)
And now it should work :)
Note: If you open an app that you used as a random app in step 3, it may not minimize perfectly to docky
Solution 2:
I am having the same or a related problem trying to minimize windows only to docky. I think I've found a solution. If you go to docky's settings and set the configuration to none then the window minimizing will only go to your dock. I am still playing with it to see if it will continue do this.
Solution 3:
Checking the animation settings in compizConfig might help.