possible bug.
I use Ubuntu 14.04 and 2 screens.
When I start the patcher it doesn't appear at all when the 2nd screen is connected, but it is running in the background.
When I use multiple workspaces (and 2 screens): Axoloti program shows up at workspace 3 , but every time an extra window is opened (or a popup appears) it starts at workspace 1, so I'm constantly moving windows.
It seems to work fine when I disable the 2nd monitor.
(possible solution: http://askubuntu.com/questions/231296/java-application-appears-in-other-unity-workspace )