The get_map function is called right where the setting exists. You can see that in admin/admin.php.
And this is something that we haven’t experienced on any other site (of the 1000 odd ones) that uses nginx-helper (including our own network).
So, shooting an arrow, in dim light, I assume that somehow the function is not able to get to the database table (prefix_blogs). The log entry shows that the function update_map was called, which in turn, first calls the get_map to get the map and then rewrites the map.conf./
For some reason, get_map is returning nothing and hence update_map fails, as well.
To test this, replace
return 'any random string';
The random string would show up in the settings, as well as the map.conf.
Now, if that doesn’t happen, then kindly contact me on saurabh dot shukla at rtcamp dot com. If it happens though, kindly check if you have the wp_blogs table in your database. In any case, you can send me an additional admin credentials on the email address and I can look into it personally.