Having the same issue. But actually, reading this post, I realized that model is not wrong and Known WS condition is not missing. In the 2D manual its written that when a stage hydrograph is inserted, stages above the terrain will put in flow into the system and stages below the terrain will draw it out.
That means that if you have a WS wich is higher than terrain you will always flow going inside the model. And it does make sense because water cant find an exit over there, therefore it has to got out trhough the flood plains.
Do you guys think im right with this poor reasoning?? Im having so much problems with the Output boundary conditions in unsteady models.