The kernel code, when setting the BIOS clock notes that the clock time
ticks to the next second 0.5 seconds after adjusting it (see
linux/arch/i386/kernel/time.c).
hwclock --systohc sets the CMOS clock at the 1 second boundry and thus
causes the clock to be wrong by 500ms each time it is reset. If the
clock is set every shutdown then the clock will have a reboot-count
related drift as well as the natural drift problems of the clock. Note
that this also mucks up the drift calculations, of course.