What architecture?
What kernel version?
Are you in fact running xntpd?

> According to the notes in the code, this should work if my RTC
> is less than 15 minutes off... which I can guarantee it is.

Well, since you looked at the source:
For some randomly chosen kernel version and architecture it does

        if (abs(real_minutes - cmos_minutes) < 30) {
                update_cmos()
        } else {
                printk("set_rtc_mmss: can't update from %d to %d\n",
                       cmos_minutes, real_minutes);
        }

so if your cmos time is 0.001 sec ahead of your system time
then around the hour you'll see
        set_rtc_mmss: can't update from 0 to 59

Of course, messing with the cmos clock at all was a rather bad idea,
but that is a different discussion.

Andries
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