If there is a default domain, skip that. Don't add it as an exception.

DNSCrypt-Preference-Pane/DNSCrypt/extra/usr/scripts/exceptions-add.sh

@@ -23,10 +23,15 @@ name_servers=$(get_dhcp_dns || get_gw)
 
 [ x"$name_servers" = 'x' ] && exit 0
 
-mkdir -p "$RESOLVER_DIR" || exit 1
+default_domain=$(./get-current-default-domain.sh)
 
+mkdir -p "$RESOLVER_DIR" || exit 1
 name_server="$gw"
 for domain in $DOMAINS_EXCEPTIONS; do
+  if [ x"$default_domain" != 'x' ]; then
+    echo "$domain" | grep -c ".*${default_domain}" > /dev/null
+    [ $? = 0 ] && continue
+  fi
   echo '# automatically generated by the dnscrypt user interface' \
     > "${RESOLVER_DIR}/${domain}"
   for name_server in $name_servers; do