In Linux Ubuntu the Alt key is reserved for dragging windows as default. therefor you can use the super(windoes) key instead for Navigating the zoom windows.
But in Ubuntu Unity the super key is used for the launcher so this gives problems as well. I found this soulutiion.
I installed the "CompizConfig Settings Manager" from "Ubuntu software center"
Goto Category "Windows Management"
choose Move Window
Change the Key-binding from alt to Super. Now you can move windows with the super key(and access launcher in Unity) and use the alt key for navigation in TVPaint.