When you model a compartment in the GMF Graph model, you are able to define a layout in the referenced figure. I.e. in Seff editor, we use a GridLayout. By default, the generated GMF code does not support any other layout then ListLayout and XYLayout. As a result, your GridLayout will lead to a non-editable compartment. It will be shown, but you will not able to move the included elements for example.
As a solution, you will need to disable the default ListLayout in the gmfgen model manually. Note: This manual change is kept when you recreate the gmfgen model from the gmfmap model, as long as you do not delete it and build it from scratch.
To diable the ListLayout, open your gmfgenmodel. Navigate to the Gen Editor -> Gen Diagram -> Gen Compartment, that you want to modify. Open the properties view and change the property ListLayout from true to false.