The clock (timer 2) speeds up by a factor of 5 or so.
I can only assume that the firmware uses it for something
to do with detecting the lid opening again.

Timesync doesn't change the local hardware, it just
tweaks the kernel's idea of what time it is and of
what the clock frequency is.  It would cope with
the clock change except that I made timesync ignore any huge
swings (anything more than 25%) because I had assumed that
would only be the result of a samplng mistake.

I changed the limits and timesync will now put up with such a
change, though it will take some minutes to latch onto
the exact new value (needs enough of a time base to
compare to).

Tell me if this is a problem.  Short of actually
implementing ACPI, I think this is as good as we can
do.