When checking "sync everything", only check the other boxes which are visible...

chrome/browser/sync/resources/configure.html

Index: chrome/browser/sync/resources/configure.html
===================================================================
--- chrome/browser/sync/resources/configure.html	(revision 64650)
+++ chrome/browser/sync/resources/configure.html	(working copy)
@@ -187,18 +187,22 @@
     setChooseDataTypesCheckboxes(args);
     setEncryptionCheckboxes(args);
     setErrorState(args);
-  }
-
-  function checkAllDataTypeCheckboxes() {
-    var checkboxes = document.getElementsByName("dataTypeCheckbox");
-    for (var i = 0; i < checkboxes.length; i++) {
-      checkboxes[i].checked = true;
-    }
-  }
-
-  function setCheckboxesToKeepEverythingSynced(value) {
-    setDataTypeCheckboxesEnabled(!value);
-    if (value)
+  }
+
+  function checkAllDataTypeCheckboxes() {
+    var checkboxes = document.getElementsByName("dataTypeCheckbox");
+    for (var i = 0; i < checkboxes.length; i++) {
+      // Only check the visible ones (since there's no way to uncheck
+      // the invisible ones).
+      if (checkboxes[i].parentElement.className == "sync-item-show") {
+        checkboxes[i].checked = true;
+      }
+    }
+  }
+
+  function setCheckboxesToKeepEverythingSynced(value) {
+    setDataTypeCheckboxesEnabled(!value);
+    if (value)
       checkAllDataTypeCheckboxes();
   }
 
@@ -302,7 +306,8 @@
     var atLeastOneChecked = false;
     var atLeastOneEnabled = false;
     for (var i = 0; i < checkboxes.length; i++) {
-      if (!checkboxes[i].disabled && checkboxes[i].style.display != 'none') {
+      if (!checkboxes[i].disabled &&
+          checkboxes[i].parentElement.className == "sync-item-show") {
         atLeastOneEnabled = true;
         if (checkboxes[i].checked) {
           atLeastOneChecked = true;