--- xpra-0.16.2/setup.py
+++ xpra-0.16.2/setup.py
@@ -1723,8 +1723,8 @@
         #prepare default [/usr/local]/etc configuration files:
         if '--user' in sys.argv:
             etc_prefix = 'etc/xpra'
-        elif sys.prefix == '/usr':
-            etc_prefix = '/etc/xpra'
+        elif sys.prefix[-4:] == '/usr':
+            etc_prefix = sys.prefix[:-4] + '/etc/xpra'
         else:
             etc_prefix = sys.prefix + '/etc/xpra'
 
--- xpra-0.16.2/xpra/platform/paths.py
+++ xpra-0.16.2/xpra/platform/paths.py
@@ -40,9 +40,9 @@
 def do_get_system_conf_dirs():
     prefix = get_install_prefix()
     #the system wide configuration directory
-    if prefix == '/usr':
+    if prefix[-4:] == '/usr':
         #default posix config location:
-        return ['/etc/xpra']
+        return [sys.prefix[:-4] + '/etc/xpra']
     #hope the prefix is something like "/usr/local" or "$HOME/.local":
     return [prefix + '/etc/xpra/']