--- javascript_aggregator.module
+++ javascript_aggregator.module
@@ -32,6 +32,23 @@
 }
 
 /**
+ * Implementation of hook_theme_registry_alter().
+ *
+ * Make javascript_aggregator's page preprocess function run *after* everything else's (even jQuery Update),
+ * so that a theme can't call drupal_get_js() and mess everything up.
+ */
+function javascript_aggregator_theme_registry_alter(&$theme_registry) {
+  if (isset($theme_registry['page'])) {
+    // If javascript_aggregator's preprocess function is there already, remove it.
+    if ($key = array_search('javascript_aggregator_preprocess_page', $theme_registry['page']['preprocess functions'])) {
+      unset($theme_registry['page']['preprocess functions'][$key]);
+    }
+    // Now tack it on at the end so it runs after everything else.
+    $theme_registry['page']['preprocess functions'][] = 'javascript_aggregator_preprocess_page';
+  } 
+}
+
+/**
  * Implementation of hook_preprocess_hook().
  *
  * Minify the aggregated JavaScript file if JavaScript Optimization is turned on.