I'm continuing to experiment with SPheno versions with CKM matrix. What I observe is that whether or not of diagonal (tree-level) decays work is connected with the order of fields in the Yukawa interactions. Take for example the build in SM. The Yukawa terms there are
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LagHC = -(Yd conj[H].d.q + Ye conj[H].e.l + Yu u.q.H);
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LagHC = -(Yd conj[H].q.d + Ye conj[H].e.l + Yu H.q.u);
cheers,
Wojciech