The Asus P6T and Lian Li PC-B70 as in my specs below.
I've seen the pinout you found at the Asus board and others as well but I would not do a re-wire by them. The idea that the headphone connector or wire is somewhere damaged is a possibility, but if you don't see any damage like a cut in the wire, something smashed, or anything melted, then I'd doubt that.
The email you received from Lian Li is something I thought of at the first, that being that Windows is shutting down because of a conflict with the audio card. But why only while using the I/O panel headphone connector, and not when using the port on the back of the card? It is a strange problem and I would keep investigating but suggest meanwhile using the port on the back of the card.
I didn't connect everything in the Lian Li I/O panel because I ran out of connectors for example for the esata wire; where headphones are concerned I have a connector on the Klipsch control module that came with the speaker system. These wires I just cable tied up and stuck away in the back side of the case.
I'd send an email to Asus requesting a schematic of the card and see if they respond.