Ok. I can reproduce this problem now (have to create same hierarchy like
you).
If you open .log file you'll see ClassCast exception there and this is a
reason for problems with setting custom layout.
Workarounds:
1. add removeEditPolicy(EditPolicy.LAYOUT_ROLE); call to the end of createDefaultEditPolicies()
method in CompartmentEditPart
2. or open .gmfgen model, locate two (both) GenCompartment instances there
and set "ListLayout" property to "true". (looks like Q&A was written for
the case of compartment with list layout).