Index: src/main/java/com/xpn/xwiki/plugin/packaging/Package.java
===================================================================
--- src/main/java/com/xpn/xwiki/plugin/packaging/Package.java	(revision 4194)
+++ src/main/java/com/xpn/xwiki/plugin/packaging/Package.java	(working copy)
@@ -574,6 +574,15 @@
                 if (!backupPack) {
                     doc.getDoc().setAuthor(context.getUser());
                 }
+                
+                if ((doc.getDoc().getDocumentArchive() == null)
+                    || (doc.getDoc().getDocumentArchive().getRCSArchive() == null)) {
+                    // doc.version will be out of sync with archive.version 
+                    //  if we leave doc.version>1.1 when archive is empty
+                    //if (!preserveVersion) {   
+                        doc.getDoc().setVersion("1.1");
+                    //}
+                }
 
                 // We don't want date and version to change
                 // So we need to cancel the dirty status
@@ -584,13 +593,12 @@
                 context.getWiki().saveDocument(doc.getDoc(), context);
                 doc.getDoc().saveAllAttachments(context);
 
+                // if there is no archive in xml and content&metaData Dirty is not set
+                //  when archive was not saved
+                //  so we need save it via resetArchive
                 if ((doc.getDoc().getDocumentArchive() == null)
-                    || (doc.getDoc().getDocumentArchive().getRCSArchive() == null)) {
-                    if (!preserveVersion) {
-                        doc.getDoc().setVersion("1.1");
-                    }
+                    || (doc.getDoc().getDocumentArchive().getRCSArchive() == null))
                     doc.getDoc().resetArchive(context);
-                }
             } catch (XWikiException e) {
                 addToErrors(doc.getFullName() + ":" + doc.getLanguage(), context);
                 if (log.isErrorEnabled()) {
Index: src/main/java/com/xpn/xwiki/XWiki.java
===================================================================
--- src/main/java/com/xpn/xwiki/XWiki.java	(revision 4194)
+++ src/main/java/com/xpn/xwiki/XWiki.java	(working copy)
@@ -908,8 +908,10 @@
                 context.setDatabase(server);
             }
 
-            // Setting comment before saving
+            // Setting comment before saving. do not modify metadatadirty.
+            boolean isMetaDataDirty = doc.isMetaDataDirty();
             doc.setComment((comment == null) ? "" : comment);
+            doc.setMetaDataDirty(isMetaDataDirty);
 
             getStore().saveXWikiDoc(doc, context);