I'll give the suggestions above a go when I get the system back.Once again, thanks so much for reporting the issue and help with testing! I know going through remote diagnostics is a pain, especially when you have a workaround. :) Anyway, your help here is very much appreciated.
Right now it's out on loan for application testing.
And there is a simple workaround for that system, which I'm now using:
just disable the RTC Alarm in the BIOS and the issue goes away.
And as you point out, hwclock does seem to be diddling with the Alarm
for some reason, so I'm feeling this isn't so important any more.
But as we've gone this far, I will instrument things as requested
when I get the system back in a few days.