Index: src/main/java/org/apache/jackrabbit/filevault/maven/packaging/VaultMojo.java
===================================================================
--- src/main/java/org/apache/jackrabbit/filevault/maven/packaging/VaultMojo.java	(revision 1869519)
+++ src/main/java/org/apache/jackrabbit/filevault/maven/packaging/VaultMojo.java	(working copy)
@@ -28,6 +28,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.stream.Collectors;
 
 import javax.annotation.Nonnull;
 
@@ -270,7 +271,10 @@
                 }
 
                 // check for uncovered files (i.e. files from the source which are not even added to the content package)
-                Collection<File> uncoveredFiles = getUncoveredFiles(jcrSourceDirectory, Constants.ROOT_DIR + "/" + prefix, contentPackageArchiver.getFiles().keySet(), null);
+                Collection<String> entryNames = contentPackageArchiver.getFiles().keySet().stream()
+                        .map(name -> FilenameUtils.separatorsToUnix(name))
+                        .collect(Collectors.toList());
+                Collection<File> uncoveredFiles = getUncoveredFiles(jcrSourceDirectory, Constants.ROOT_DIR + "/" + prefix, entryNames, null);
                 if (!uncoveredFiles.isEmpty()) {
                     for (File uncoveredFile : uncoveredFiles) {
                         getLog().warn("File " + uncoveredFile + " not covered by a filter rule and therefore not contained in the resulting package");