So strange
When you press a button on any remote, a transmitter within the remote emits the command either as a Light Wave or Radio Wave.
• Light Wave, Infrared, InfraRed, IR
• Radio Wave, Radio Frequency, RF
Infrared is like a flashlight because you have to aim (shine) the remote at the component.
This is why the Pairing steps begin with "Point the remote at the receiver with a clear line of sight" because the pairing begins in Light mode. In Light mode, the remote is getting the attention of the specific Contour box. ("Hey, you")
I suspect when you "Press the Voice Command button to begin programming the remote," the remote then goes into Radio mode. After getting the attention of the Contour box via Light, the remote then pairs the box via Radio.
Most TV sets only have Light sensors to receive commands via IR so after you pair the remote to a TV set, the remote emits the applicable commands via Light.
Contour, however, also has a radio receiver so the remote emits the applicable command for Contour via Radio.
As opposed to directly aiming for Light, Radio Wave emits from the remote in all directions like a bubble. In addition to emitting in all directions, these low-frequency Radio Waves from the remote can also penetrate walls, floors, furniture, etc. (Beginning to see the Light?)
Therefore, while upstairs pairing a device via Radio Waves and if you can imagine through your walls, floors, etc the direction and location of the downstairs receiver, it's probably within 50 feet.
If any Contour box is within 50 feet of your upstairs remote and senses commands via Radio Waves, it thinks the commands are for it. However, pressing the Contour button (again, again, again) narrows the Radio Waves to the specific frequency of the intended Contour box.