They go from the socket to the two switches and then to the SNES slot.
You can also try to hold the flash adapter upright in the cart slot while reading the ID to see if maybe there is a problem with the cart slot connecting to the flash adapter, the added weight of the socket might make the adapter lean towards one side.
Also make sure that your Cart Reader is set to 3.3V as the MX29LV160 is a 3.3V flashrom.