latency issues (practical aid needed on a practical example)

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Hi everyone!
   I just compiled a sound generator, which can be controlled vai MIDI, it uses 
simpe raw-midi and jack as output, via bio2jack.
   Now I have horrible latency 0.2-0.5sec (rough estimate). Where should I 
start looking in my setupt. I know others had the software running without 
problems.
   Sorry for being so abstract, but I'm not allowed to mention the software. 
:-( But I could post parts of the source if necessary.
   My setup is:
Debian Lenny with custom built kernel 2.6.24-rt1
   JACK subversion 0.109.0
   jack-commandline:
jackd --timeout 4500 -R -d alsa -d hw:1 -r 48000 -p 128 -H -M -z shaped
   ALSA version 1.0.15
   Any idea where to optimise?
   Kindest regards
          Julien

--------
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