Well, just an update: you can disable hpet by adding hpet=disable to the kernel 
boot line in grub's menu.lst.
I added that hpet=disable to the kernel and no luck. The PC didn't wakeup.

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[INTREPID] /sys/class/rtc/rtc0/wakealarm is not working
https://bugs.launchpad.net/bugs/259149
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