The plugin settings & Google accounts/locations are saved for each site in the network individually so that shouldn’t cause such a conflict…
Have you ever selected the other location (B) on that site before, and then switched it back to A?
The locations are identified internally by their Google ID which is a very long string of numbers. So its unlikely that the plugin would post to the incorrect location by itself, unless it has stored the ID of the wrong location in the database somewhere.
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Are you running the latest version (3.0.14) and have you refreshed the location list afterwards, and then saved the settings? There was a small issue in 3.0.10-3.0.12 that could cause locations within location groups to be selected incorrectly.
Note: if you do not have the plugin network activated and its not active on the main site of the network, update notifications will not show up in the Network Admin.