diff --git a/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/ash-template b/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/ash-template
index 9efd69686..4d7838dc9 100644
--- a/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/ash-template
+++ b/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/ash-template
@@ -40,7 +40,7 @@ fi
 
 # Loads a configuration file full of default command line options for this script.
 loadConfigFile() {
-  cat "$1" | sed '/^\#/d' | sed 's/^-J-X/-X/' | tr '\r\n' ' '
+  cat "$1" | sed '/^\#/d;s/\r$//' | sed 's/^-J-X/-X/' | tr '\r\n' ' '
 }
 
 
diff --git a/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/bash-template b/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/bash-template
index 4957421c3..72fe27b24 100644
--- a/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/bash-template
+++ b/src/main/resources/com/typesafe/sbt/packager/archetypes/scripts/bash-template
@@ -263,7 +263,7 @@ run() {
 
 # Loads a configuration file full of default command line options for this script.
 loadConfigFile() {
-  cat "$1" | sed '/^\#/d'
+  cat "$1" | sed '/^\#/d;s/\r$//'
 }
 
 # Now check to see if it's a good enough version