Hi Clemens,
If the previous error you mentioned appears in running a T2D-SIS simulation, it's normal as you're using the Soulsby-Van Rijn transport formulation that requires waves data. For this 2-way coupling test, you can just switch to the Meyer-Peter (BED-LOAD TRANSPORT FORMULA=1, with EFFECT OF WAVES=NO) for instance and see what's happen.
For the 3-way coupling, I saw in your sisyphe steering file that you're also resolving the suspension transport by the explicit formulation. The Soulsby-Van Rijn transport formulation already includes the suspension transport contribution. Try to turn off the explicit suspension, or use a formulation that deals only with bed load effect (7, Van Rijn).
I hope it helps,
Laurent