Using an older "known-good" kernel, could you build and run the test
case at the end of Documentation/rtc.txt a few times and see if it
triggers the same problem?
I'm suspicious that the setting the alarm is whats tripping the BIOS
into enabling the HT bit. Because with older kernels, we used PIE mode
irqs which hwclock usually uses at boot, but with newer kernels, we
emulate PIE via AIE alarm mode. So if the BIOS was broken before, you
wouldn't have noticed unless you tried to use AIE irqs.
If this doesn't work, I'll get some patches to both 2.6.27 and 2.6.28
kernels to debug the exact flow of how we're touching the hardware and
then we can further narrow it down.