With the default settings Enterprise Architect will only run in full screen mode. This makes further problems when using pop up windows like test or the maintenance window. They might not show up properly.
To fix this open the Wine configuration for the bottle containing Enterprise Architect. Go to the Graphics tab and click to allow the window manager to control the windows. This will allow to run Enterprise Architect in a resizable window and will also fix the problem with the pop up windows like test and maintenance.