Dear Simon,
Caveats: I'm a newbie telemac user and this will possibly be a nonsense answer to the first question.
Each time i start a "cold start" simulation in telemac2D using a prescribed steady inlet flow and a prescribed constant elevation output (to generate a "steady" hotstart for the real simulation) in Fudaa-Prepro i enable "Intial conditions" and give a positive and reasonable "FREE SURFACE" elevation along the inlet boundary, so telemac has some water to move.
I assume this procedure is taken by telemac2d/3D as a "suggestion" rather than an imposed condition (because the real imposed condition is the flow magnitude), so generally in the output file this free surface is different, and i asume this one the "appropriate one" to start the real (unsteady) simulation.
I also remember reading somewhere in Fudaa options that having a "prescribed elevation" and a "prescribed flowrate" at the same time in a boundary condition is not "yet" implemented (over constrained system maybe?).
I hope someone with more knowledge of the telemac system can properly answer this post...
Regards,
José.