As you can see, splitting both culverts in three doesn't just damp oscillations, it also changes the capacity.
I suspect volume limitation because of spatial discretization :
QMAX1=0.9D0*H(I1)*V2DPAR%R(I1)/DT
It means that at each time step, no more than 90% of the available volume can be used by the culvert.
To damp oscillation (but doesn't change the value and the limitation), you can change Relaxation coefficient (0.1 or 0.2 instead of 0.5).
I don't think hydraulic radius is the reason as you consider a Manning coefficient as 0 (FRIC in your culvert file) -> No linear headloss.
Also, in your case, you should not refine your mesh around culvert ends... and will not have this volume limitation with coarce mesh (-> bigger element).
I guess CLP is just the french for "clapet" meaning valve.
Anyway :
0 = no valve
1 = flow authorized only from 1 to 2
2 = flow authorized only from 2 to 1
3 = no flow
Alexis