Index: bp-core/bp-core-templatetags.php
===================================================================
--- bp-core/bp-core-templatetags.php	(revision 2985)
+++ bp-core/bp-core-templatetags.php	(working copy)
@@ -959,7 +959,26 @@
 	}
 
 function bp_has_custom_activation_page() {
-	if ( locate_template( array( 'activate.php' ), false ) || locate_template( array( '/registration/activate.php' ), false ) )
+	global $wpdb;
+
+	$activation_pages = array( 'activate.php', '/registration/activate.php' );
+
+	if ( bp_core_is_multisite() && $wpdb->blogid != BP_ROOT_BLOG ) {
+		$stylesheet = get_blog_option( BP_ROOT_BLOG, 'stylesheet' );
+		$stylesheet_root = get_theme_root( $stylesheet );
+
+		$template = get_blog_option( BP_ROOT_BLOG, 'template' );
+		$template_root = get_theme_root( $template );
+
+		foreach ( $activation_pages as $page ) {
+			if ( file_exists( "$stylesheet_root/$stylesheet/" . $page ) )
+				return true;
+			else if ( file_exists( "$template_root/$template/" . $page ) )
+				return true;
+		}
+	}
+
+	if ( locate_template( $activation_pages, false ) )
 		return true;
 
 	return false;