diff --git a/code/controllers/configuration/configuration.dm b/code/controllers/configuration/configuration.dm
index af88fe86840..5f9e9c51178 100644
--- a/code/controllers/configuration/configuration.dm
+++ b/code/controllers/configuration/configuration.dm
@@ -244,7 +244,7 @@
 			log_config(log_message)
 			stack_trace(log_message)
 		else
-			if(E.modified && !E.dupes_allowed)
+			if(E.modified && !E.dupes_allowed && E.resident_file == filename)
 				log_config_error("Duplicate setting for [entry] ([value], [E.resident_file]) detected! Using latest.")
 
 		E.resident_file = filename