We just had the same issue pop up last week. We were able to run our model in 4.1, but not in 5.0.3. RasMapper froze in 4.1 when we tried to do inundation boundaries, so it seems like it only ran in 4.1 because the XS Interpolation Surfaces are not calculated as part of the initial calculation as they are in 5.0.3.
We spent a while sorting our specific issue out, but we were able to get it to run and generate the XS Interpolation Surfaces by increasing the distance between our bank station points, i.e. moving them further away from the channel center. We took this to mean that there was some problem generating the TIN used for the XS Interpolation Surfaces when the bank stations are too “tight” around the channel.
Hope this helps!