diff -ru a/pkg.c b/pkg.c
--- a/pkg.c	2010-05-08 21:14:17.000000000 +0100
+++ b/pkg.c	2010-06-05 11:41:00.404180293 +0100
@@ -910,7 +910,7 @@
 		{
 		  debug_spew ("Package %s has %s in Cflags\n",
 			      pkg->name, (gchar *)iter->data);
-		  if (g_getenv ("PKG_CONFIG_ALLOW_SYSTEM_CFLAGS") == NULL)
+		  if (g_getenv ("PKG_CONFIG_ALLOW_SYSTEM_CFLAGS") == NULL && pcsysrootdir == NULL)
 		    {
 		      debug_spew ("Removing %s from cflags for %s\n", iter->data, pkg->key);
 		      ++count;
@@ -949,7 +949,7 @@
         {
           debug_spew ("Package %s has -L" SYSTEM_LIBDIR " in Libs\n",
                       pkg->name);
-          if (g_getenv ("PKG_CONFIG_ALLOW_SYSTEM_LIBS") == NULL)
+          if (g_getenv ("PKG_CONFIG_ALLOW_SYSTEM_LIBS") == NULL && pcsysrootdir == NULL)
             {              
               iter->data = NULL;
               ++count;