Up until now, unsteady flow HEC-RAS uses a very simplistic method for handling juctions. It simply projected the water surface elevation of the downstream cross section to the two cross sections upstream of the junction. For shallow, deep systems, this worked fine-no problems. However, if you tried to model a steep reach with shallow depths you run into a host of problems at junctions. I've blogged about this problem before and provided examples of ways around to work around it. However, in the new version soon to be released (4.0.1) HEC has taken care of this problem and it works quite nicely.