I did something similar. I created a bot which I named "Beacon" that creates Beacons and then puts them into the "Beacon Storage", as shown below. I was able to avoid the problem that you are having by making the "Find nearest Beacon" command centered on the spot where the Beacons are created (as indicated by the question mark (?) following the command) rather than centered on a specific Beacon (which would instead be indicated by the blue-and-red symbol) which I'm sure your "bot-beacon" has connected to its "Find nearest Beacon" command and which you said uses the "local" Beacon. Try changing your bot's commands this way. Good luck.
