See https://sixohthree.com/1595/wordpress-mu-domain-mapping-patches

arbitrary-siteurl.diff

Index: domain_mapping.php
===================================================================
--- domain_mapping.php  (revision 9545)
+++ domain_mapping.php	(revision 9553)
@@ -515,27 +515,37 @@
 }
 
-function domain_mapping_siteurl( $setting ) {
-	global $wpdb, $current_blog;
+function domain_mapping_siteurl( $setting, $blog_id = 0 ) {
+	global $wpdb, $current_blog, $switched;
 
 	// To reduce the number of database queries, save the results the first time we encounter each blog ID.
 	static $return_url = array();
 
+	if( $blog_id == 0 ) {
+		$blog_id = $current_blog->blog_id;
+	}
+
 	$wpdb->dmtable = $wpdb->base_prefix . 'domain_mapping';
 
-	if ( !isset( $return_url[ $wpdb->blogid ] ) ) {
+	if ( !isset( $return_url[ $blog_id ] ) ) {
 		$s = $wpdb->suppress_errors();
 
-		if ( get_site_option( 'dm_no_primary_domain' ) == 1 ) {
-			$domain = $wpdb->get_var( "SELECT domain FROM {$wpdb->dmtable} WHERE blog_id = '{$wpdb->blogid}' AND domain = '" . $wpdb->escape( $_SERVER[ 'HTTP_HOST' ] ) . "' LIMIT 1" );
+		if ( get_site_option( $blog_id, 'dm_no_primary_domain' ) == 1 ) {
+			if ( $switched === false ) {
+				// Only filter using HTTP_HOST if we haven't done switch_to_blog()
+				$domain = $wpdb->get_var( "SELECT domain FROM {$wpdb->dmtable} WHERE blog_id = '{$blog_id}' AND domain = '" . $wpdb->escape( $_SERVER[ 'HTTP_HOST' ] ) . "' LIMIT 1" );
+			} else {
+				$domain = $wpdb->get_var( "SELECT domain FROM {$wpdb->dmtable} WHERE blog_id = '{$blog_id}' LIMIT 1" );
+			}
+
 			if ( null == $domain ) {
-				$return_url[ $wpdb->blogid ] = untrailingslashit( get_original_url( "siteurl" ) );
-				return $return_url[ $wpdb->blogid ];
+				$return_url[ $blog_id ] = untrailingslashit( get_original_url( "siteurl", $blog_id ) );
+				return $return_url[ $blog_id ];
 			}
 		} else {
 			// get primary domain, if we don't have one then return original url.
-			$domain = $wpdb->get_var( "SELECT domain FROM {$wpdb->dmtable} WHERE blog_id = '{$wpdb->blogid}' AND active = 1 LIMIT 1" );
+			$domain = $wpdb->get_var( "SELECT domain FROM {$wpdb->dmtable} WHERE blog_id = '{$blog_id}' AND active = 1 LIMIT 1" );
 			if ( null == $domain ) {
-				$return_url[ $wpdb->blogid ] = untrailingslashit( get_original_url( "siteurl" ) );
-				return $return_url[ $wpdb->blogid ];
+				$return_url[ $blog_id ] = untrailingslashit( get_original_url( "siteurl", $blog_id ) );
+				return $return_url[ $blog_id ];
 			}
 		}
@@ -546,11 +556,11 @@
 		$protocol = ( 'on' == strtolower( $_SERVER[ 'HTTPS' ] ) ) ? 'https://' : 'http://';
 		if ( $domain ) {
-			$return_url[ $wpdb->blogid ] = untrailingslashit( $protocol . $domain  );
-			$setting = $return_url[ $wpdb->blogid ];
-		} else {
-			$return_url[ $wpdb->blogid ] = false;
-		}
-	} elseif ( $return_url[ $wpdb->blogid ] !== FALSE) {
-		$setting = $return_url[ $wpdb->blogid ];
+			$return_url[ $blog_id ] = untrailingslashit( $protocol . $domain  );
+			$setting = $return_url[ $blog_id ];
+		} else {
+			$return_url[ $blog_id ] = false;
+		}
+	} elseif ( $return_url[ $blog_id ] !== FALSE) {
+		$setting = $return_url[ $blog_id ];
 	}
 

mu-plugins-url.diff

Index: domain_mapping.php
===================================================================
--- domain_mapping.php  (revision 9553)
+++ domain_mapping.php	(revision 9554)
@@ -660,5 +660,9 @@
 // fixes the plugins_url 
 function domain_mapping_plugins_uri( $full_url, $path=NULL, $plugin=NULL ) {
-	return get_option( 'siteurl' ) . substr( $full_url, stripos( $full_url, PLUGINDIR ) - 1 );
+	if( false === ( $pos = stripos( $full_url, PLUGINDIR ) ) ) {
+		$pos = stripos( $full_url, MUPLUGINDIR );
+	}
+
+	return get_option( 'siteurl' ) . substr( $full_url, $pos - 1 );
 }
 
@@ -668,5 +672,5 @@
 
 if ( defined( 'DOMAIN_MAPPING' ) ) {
-	add_filter( 'plugins_url', 'domain_mapping_plugins_uri', 1 );
+	add_filter( 'plugins_url', 'domain_mapping_plugins_uri', 1, 3 );
 	add_filter( 'theme_root_uri', 'domain_mapping_themes_uri', 1 );
 	add_filter( 'pre_option_siteurl', 'domain_mapping_siteurl' );
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