Yes, the Load Flow (LF) analysis can be performed on a unbalanced three phase system. The Load Flow tool should find a solution just as in the balanced case.
However, in the current version of SimPowerSystems (R13), the LF solution supposes that the machines are providing balanced three phase currents. The solution is good (displayed in the load-flow tool), but the simulation will not start directly in steady-state. The initial conditions calculated by the load flow is close to the steady-state simulation: you will see a small transient at the beginning, and then the simulation rapidly converges. Consequently, you (should) have to wait for a few milliseconds of simulation before you apply a fault, or a transient, etc.
The POWERGUI tool in SimPowerSystems 4.4( R2007a ) and above can now be used for analysis so that the simulation starts in steady state.
In summary, the solution found by the load flow can be used on unbalanced systems and help to reach the steady-state rapidly.
