Why is one of my WiFi networks not visible after connecting to the other one?
How many other APs (Access Points) and devices are their in the vicinity?

If your first AP (on channel X) is causing overloading (or interference) on that channel, other APs are going to change signal strength and/or change to other channels.

Basically, you are dropping a large pebble into a small pond.  There is always going to be other effects.

If this happened under controlled conditions (i.e. out in the country), with no other signal sources or traffic, then you would have a legitimate puzzle ..