Forked server with SM, use same
...cfg/sourcemod/ configurations files.
If you want different settings to each server, you have to do this hard way.
//Disable or remove cvars what you want set different from
...cfg/sourcemod/anyconfigfile.cfg
And add these cvars to each server configuration file "serverx.cfg"
You can set to server own serverx.cfg file, add each server launch parameter
+servercfgfile "server2.cfg"
Then it start use that file all the time.
About ...addons/sourcemod/configs, it should not use same folders if you have set SM right to each server.
http://wiki.alliedmods.net/Multiple_...28SourceMod%29
So I don't know have you done this but,
copy
...addons/sourcemod folder, paste and rename folder
...addons/sourcemod2/
To server launch parameter you add
+sm_basepath addons/sourcemod2