The issue is with the .desktop file of chrome (and possibly other applications).
For example take, /usr/share/applications/google-chrome.desktop
You'll find 3 entries in this file, [Desktop Entry], [NewWindow Shortcut Group] and [NewIncognito Shortcut Group]. Make sure that under each group there's the following line, it doesn't matter where in the group it is.
The issue is with the .desktop file of chrome (and possibly other applications). applications/ google- chrome. desktop
For example take, /usr/share/
You'll find 3 entries in this file, [Desktop Entry], [NewWindow Shortcut Group] and [NewIncognito Shortcut Group]. Make sure that under each group there's the following line, it doesn't matter where in the group it is.
StartupWMClass= Google- chrome- stable
More info about plank's window matching can be found here: http:// wiki.go- docky.com/ index.php? title=How_ to_Customize_ Window_ Matching