Linux causing failing wake-on-RTC function on an ASUS A8N-SLI motherboard

Hi list,

I have an ASUS A8N-SLI nForce4-based motherboard, running Debian testing. A
few months back the wake-on-RTC function stopped working. It turns out that
something about Linux is causing this. When I boot Linux, whether I shutdown
properly or hit the power-button, wake-on-RTC won't work - the machine won't
boot at a given time like I tell it to in the BIOS. However, if after setting
the time to boot in the BIOS I switch the machine off before it gets a chance
to boot, wake-on-RTC works just fine, and also, when booted into WinXP and
shutdown properly. Interestingly, when booted to WinXP and powered-off
manually (improperly), wake-on-RTC doesn't work.

So I'm pretty perplexed. It's like there's something about the wake-on-RTC the
motherboard forgets upon booting an OS, possibly from loading a driver, and
WinXP, but not Linux, remembers to set it back when shutting down. Or
something.

I have a feeling it might've started around when the kernel went from 2.6.16
to 2.6.17, but I'm not sure.

Anyone have any ideas where I should look? Who I should ask?

Peace,
Brendon