Sorry for re-floating this thread... but only Claude answer it and he was talking about previous version of Pd, so, it doesn't apply in my Pd-Extende version. I paste again the mail:

-------- Mensaje original --------
Asunto: Worse performance with -nogui.
Fecha: Thu, 15 Aug 2013 01:22:36 -0300
De: Mario Mey <mariomey@gmail.com>
Para: pd-list <pd-list@iem.at>


Two issues:

First at all, when trying my patch (MEH-SYSTEM) with -nogui option, I 
was having a "Segment fault"... untill I discovered that the "Robot" FX, 
from RJDJ was turning DSP on.... and DSP was already on (was turned on 
with a [loadbang]-[delay 2000]). This crashed Pd. Maybe a bug...?

Attempting to save some CPU (-nogui option), I started using the patch 
and recorded all the sample banks... then, a lot of noisy clicks started 
to appear. If I mute all the banks, the clicks are there, at low volume 
but very audible.

Then, I realized that that noise is there only with -nogui option. Using 
GUI, it sounds great. Is this a known issue? Because I expected to have 
the opposite result...

I'm using Pd-Extended 0.43.4, Ubuntu 12.04, Jackd (Jack2?) with 
256frames, 2periods, 48000, PulseAudio uninstalled, with a USB soundcard 
(Encore ENMAB-8CM). It does the same noise with the integrated soundcard.

Here is the WIP (last version: 0.91):
http://puredata.hurleur.com/viewtopic.php?pid=37430

If I can give you any other information, just ask for it.

EDIT: I'm trying to get no noise, because I'm trying to use 128 frames in Jack, instead of 256, to get less latency.