Actually, looking closer at the new pics, it is not a mux, but some sort of protection/signal conditioning device. In that case layout makes a bit more sense. It just passes all 3 diff pars through without doing any switching. The left two pairs are USB3 signals, and the right one going to the choke is USB2.
It might help to remove it to see the exact pin layout. It looks like something custom. But also, simply removing it might fix your issue. If the traces simply go though under the IC, then it is likely that IC is shorting something and removing it will remove shorts.
This IC did its job and protected the rest of the components (hopefully).
And actually my initial though about the mux was completely wrong. Assuming that this is a USB3 B connector, it is not reversible, so there is no need for a mux at all.