clear region map as well
diff --git a/bundles/org.eclipse.jst.jsp.core/src/org/eclipse/jst/jsp/core/internal/validation/JSPDirectiveValidator.java b/bundles/org.eclipse.jst.jsp.core/src/org/eclipse/jst/jsp/core/internal/validation/JSPDirectiveValidator.java
index 83c8f79..83febf5 100644
--- a/bundles/org.eclipse.jst.jsp.core/src/org/eclipse/jst/jsp/core/internal/validation/JSPDirectiveValidator.java
+++ b/bundles/org.eclipse.jst.jsp.core/src/org/eclipse/jst/jsp/core/internal/validation/JSPDirectiveValidator.java
@@ -162,9 +162,12 @@
 	 * batch validation call
 	 */
 	protected void validateFile(IFile f, IReporter reporter) {
-		// when validating an entire file
-		// need to clear dupes or else you're comparing between files
+		/*
+		 * when validating an entire file (or multiple files), need to clear
+		 * dupes or else you're comparing between files
+		 */
 		fTaglibPrefixesInUse.clear();
+		fTextRegionToDocumentRegionMap.clear();
 		reporter.removeAllMessages(this);
 
 		// for batch validation
@@ -183,7 +186,7 @@
 					region = region.getNext();
 				}
 
-				if(!reporter.isCancelled()) {
+				if (!reporter.isCancelled()) {
 					reportDuplicatePrefixes(f, reporter, structuredDocument);
 				}
 			}