Too bad bugzilla.kernel.org has now been down for so many weeks... so
this issue can't be taken to where it probably should really be
discussed.

Here is the workaround I'm now using:

I'm writing the desired wakeup time both to
/sys/class/rtc/rtc0/wakealarm and to a file on the file system
(/etc/wakeup_time) and in /etc/rc.local I included:

"cat /etc/wakeup_time  > /sys/class/rtc/rtc0/wakealarm"

This seems to work reliably enough, but still it's just a workaround and
people will loose time by stumbling upon this bug, as I did.

This problem seems to exist for years already, according to some
reports. More than a year ago I set up a dual-boot PPC Mac mini to wake
up on certain days to record certain radio shows, and I noticed I could
not boot Linux anymore because that reset the programmed wakeup time.
That system did not have ACPI of course, and I thought booting Mac OS
was required to refresh the RTC on every reboot... but maybe it was just
this issue.

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https://bugs.launchpad.net/bugs/403918

Title:
  ACPI Wakeup reset during reboot

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