I'm seeing this unwanted behaviour eversince Unity came to Ubuntu. The Unity's Launcher randomly "steals" the endpoint for the minimizing animations from Docky. In other words, when I click on an icon in Docky to minimize a window, that window minimizes to Unity instead of Docky. That happens most of the time to all of the windows, although sometimes, also randomly, it happens that the windows minimize to Docky, but very rarely.
Here's how it looks when I minimize a window: Here's how both animations should look:
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
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
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.
Checking the animation settings in compizConfig might help.
http://www.hackourlife.com/awn-vs-cairo-dock-vs-docky-mac-style-linux-docks-reviewed/
have you tried one of the alternatives? (ie. awn? / cairo?)
*(i used to use awn and can speak for its ease on the old 10.10 environment, but haven't attempted since the changes went in to x in 11.04< ... but i'm it's still; stable at least.)
while i know this isn't a direct fix to your problems, it may be a good temporary alternative. :D
Well, the best thing you can do is to disable the Unity plugin using CCSM. This will remove the Unity launcher, but the upper panel would disappear too. Then, install gnome-panel:
And add it to start-up applications. Log out andd then log back in.
That should solve your problem.
What I noticed (in case someone is still wondering), when the app you are minimizing is already docked to unity launcher it no longer minimizes to the launcher but instead to the dock, so to fix it I docked every single program i ever opened to launcher to avoid it being minimized to the wrong place. Seems to stop working when you move the window of the application you launched, unity seems to take over control of the app again and minimizes to the wrong place again, so unless someone knows how to fix that then this only works partially, sorry