are you aware that I was talking about electrical nets. In your example I see "normal physical" nets.
(el.net) SD2_REFCLK2_P^^^ = (phy. net) SD2_REFCLK2_P + capacitor + (phy.net) SD2_REFCLK2Q_P
May this be the difference. Try packaging your design, so that CES sees the electrical nets. Do not do this in DxD without packaging.
Yes, now I have the same problem as you