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I'm using a 22 year old Roland RD300s keyboard that sends an "all notes off" message when all notes have been released. (I can monitor the midi stream in Pianoteq). I learned from another post I made on the LinuxMusician forum concerning problems I had with Linuxsampler and sustain pedals, that in current midi practice, that the "all notes off" is an emergency signal and that normally only individual note no/off messages should be sent.

I made a test recording in Qtractor using VMPK as the keyboard (it does not send "all notes off" signals) and the playback to Pianoteq was fine. What does not quite make sense is why Pianoteq plays correctly when playing directly from Roland keyboard but does not when playing from a recorded midi from Qtractor. However, whatever it is the VMPK test suggests that the problem is the "all notes off" messages.

It also turns out that the "all notes off" messages were preventing the sustain pedal from working in linuxsampler which was the subject of my LinuxMusicians post.

... later that same day ...
I did some googling and found a program called mididing (http://das.nasophon.de/mididings/) which does filtering of midi streams. Below is a mididings script to removes the "all notes off" signals from my midi stream so that the sustain pedal now works correctly in Qtractor and linuxsampler. (note: "all notes off" == control signal 123):

#!/usr/bin/python
from mididings import *
run( Filter(CTRL) % ~CtrlFilter(123) )

(mididings creates Alsa midi in/out ports to connect with keyboard)