Periodic timing varies across boots

[C Smith <csmithquestions@gmail.com>]

I am using Xenomai 2.6.5, x86 32bit SMP kernel 3.18.20, Intel Core
i5-4460,  and I have found a periodic timing problem on one particular type
of motherboard.

I have a Xenomai RT periodic task which outputs a pulse to the PC parallel
port, and this pulse is measured on a frequency counter. This has been
working fine for years on several motherboards. I am able to adjust the
period of my task to within +/-10nsec, according to the frequency counter.
I can calibrate the periodic timing down to a period +/-10nsec on this
motherboard, and I cna restart my xenomai process many times and the timing
is fine. But if I cold-reboot the machine the measured period is wrong by
up to  +/-300nsec. Thus I cannot get consistent periodic timing from day to
day without recalibrating, which is unacceptable in my application.

In my kernel config, I am using the TSC: CONFIG_X86_TSC=y
I use rt_timer_read() to determine what time it is, and my periodic task
sleeps in a while loop, like this:
      next += period_ns + adjust_ns;
      rt_task_sleep_until(next);

I don't know what to test. Can you suggest anything?

Thanks,
-C Smith