I sometimes had problems with the constraint condition of BCs (for seepage face nodes FEFLOW does set a 1. kind BC with the head equals the z-coorinate of the node and applies a constraint that will no infiltration will be allowed). If your head is below the z-coordinate, the 1. kind BC will be converted to a 4. kind BC with flux=0, if the heads gets above and the constraint is chacked again the BC is reconverted to a 1. kind BC. In steady state models it could happen, that there is a convertion of the whole problem before all of the BCs have there finally state.
What you can do is, that you rerun the model sometimes and check whether something is changing. Or you can run the model in a quasi-steady-state (transient run with steady BCs) here the constraints are at least checked every timestep.