I guess you are using
Map configs with prefix support 1.3?
For example.
server.cfg in
/cfg
and
ba_.cfg,
ba_yard_.cfg,
ba_yard_v2.cfg in
cfg/sourcemod/map-cfg
If the map ba_yard_v2 is started, the server will execute server.cfg, then ba_.cfg, then ba_yard_.cfg, then ba_yard_v2.cfg etc. So map specific configuration will overwrite for example a ba_.cfg which is valid for all ba_*.maps