Info about my system:
Debian Squeeze, Linux 18.104.22.168-rtai x86_64 running on Intel Atom board.
Mesa 7i43 anything I/O board connected through a parallel port
LinuxCNC 2.6.0~pre (got from git, don't remember the commit)
4 identical stepper motors, drives are obviously controlled by the Mesa board.
I did the following:
1) created a 3 axis and 1 spindle configuration with PNCConf.
2) tested the XYZ axes with an oscilloscope, the signal is excellent, timings are set up well
3) when tried to test the spindle, it seemed that nothing works. AXIS just checks the "brake" checkbox and on oscilloscope I did not see any signal, even a noise.
4) after spending lot of time on IRC and trying to do various setups, I just downgraded to LinuxCNC 2.5.1 stable. Everything worked, excellent signal on spindle pins.
Below are links to INI and HAL files generated by PNCConf (2.6.0~pre version) and to a screen capture of what I did and how AXIS behaved on non-working configuration (5mb only).