I just experienced similar problem with acpi wakeup. I followed steps
found on http://www.mythtv.org/wiki/index.php/ACPI_Wakeup:

1) set alarm timestamp
$ sudo sh -c 'echo "+00-00-00 00:05:00" > /proc/acpi/alarm'

2) checked
$ cat /proc/acpi/alarm
2008-09-20 14:56:33

3) shutdown
$ sudo shutdown -h -P now

However, computer didn't start at given time. I entered BIOS UI and
found the problem is in wake-up date which was not set to 20 (day of
month) but remained unchanged  =1.  Wake-up time was set correctly. When
I manually changed wake-up date and repeated procedure then computer
started as expected. I tried to resolve this issue by updating BIOS
version but without success.

System: 8.04 (hardy), kernel 2.6.24-19-generic
Motherboard: Asus A7V8X-X, tested BIOS versions - 8 and 11

I'd be happy to provide more files and logs if they will help.

-- 
[GUTSY]  RTC alarm does not retain setting from /proc/acpi/alarm
https://bugs.launchpad.net/bugs/139846
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