The patent says:
However, there are particular devices that do not follow the IEEE 802.3 Auto-Negotiation Protocol, and are instead forced into either 10 Mbps or 100 Mbps operation. Customers who use the Auto-MDI/MDIX algorithm have grown used to not requiring special crossover cables with products that implement the algorithm. When they force speed/duplex for some limited applications, the algorithm breaks down and link is not established. The root of the problem lies in the Auto-Negotiation state machine which turns off an auto-negotiating (AN) transmitter if it detects non-FLP (non Fast Link Pulse) energy on the wire (as occurring during forced mode). When that AN transmitter is turned off, it will cause the Auto-MDI/MDIX node to incorrectly determine its link state and cycle endlessly. The logical elements described below will allow operation of Auto-MDI/MDIX with nodes that are Auto-Negotiating even when the node in question is operated in forced mode.
So if you set the speed/duplex manually, that turns off autonegotiation, and changes the signal on the wire. That causes the other end to turn off autonegotiation as well. The Auto-MDI/MDIX algorithm can no longer work out whether it has a link or not and cannot function.
(The patent basically covers "try swapping the connection pairs, randomly, every few miliseconds, until a link is established")