diff --git a/src/main/scala/com/typesafe/sbt/packager/archetypes/scripts/ApplicationIniGenerator.scala b/src/main/scala/com/typesafe/sbt/packager/archetypes/scripts/ApplicationIniGenerator.scala
index 5347fab68..ef280344b 100644
--- a/src/main/scala/com/typesafe/sbt/packager/archetypes/scripts/ApplicationIniGenerator.scala
+++ b/src/main/scala/com/typesafe/sbt/packager/archetypes/scripts/ApplicationIniGenerator.scala
@@ -21,25 +21,17 @@ trait ApplicationIniGenerator {
           val pathMapping = cleanApplicationIniPath(location)
           //Do not use writeLines here because of issue #637
           IO.write(configFile, ("# options from build" +: javaOptions).mkString("\n"))
-          val filteredMappings = universalMappings.filter {
-            case (`configFile`, `pathMapping`) =>
-              // ignore duplicate application.ini mappings with identical contents
-              // for example when using both the BASH and BAT plugin
-              false
-
-            case (_, `pathMapping`) =>
-              // specified a custom application.ini file *and* JVM options
-              // TODO: merge JVM options into the existing application.ini?
-              log.warn("--------!!! JVM Options are defined twice !!!-----------")
-              log.warn(
-                "application.ini is already present in output package. Will be overridden by 'javaOptions in Universal'"
-              )
-              false
-
-            case _ =>
-              true
+          val hasConflict = universalMappings.exists {
+            case (file, path) => file != configFile && path == pathMapping
+          }
+          // Warn the user if he tries to specify options
+          if (hasConflict) {
+            log.warn("--------!!! JVM Options are defined twice !!!-----------")
+            log.warn(
+              "application.ini is already present in output package. Will be overridden by 'javaOptions in Universal'"
+            )
           }
-          (configFile -> pathMapping) +: filteredMappings
+          (configFile -> pathMapping) +: universalMappings
 
       }
       .getOrElse(universalMappings)