I turned one of the boards I got back from OSHPark into a display for one of my stratum 1 NTP servers, so it could do double duty as an actual clock. One little gotcha with the GPS receivers I use is that sometimes they're two seconds fast for about 10 minutes. I attribute this to something to do with leap seconds - some bit of data relevant to leap seconds is only transmitted every ten minutes or so, and until the receiver gets it...
So what happened was that the clock showed time two seconds fast for a while, then the display froze for two seconds and then picked up again.
I'm pretty sure what happened was that the alarm system is set up to wake up at just the right moment to update the display. But if in the meantime the time has moved backwards, now you've got an alarm set for way in the future.
I'm going to just let that one go. In general, the clock shouldn't need to be horsed around like that too much. And if you do, and the display gets stuck, you can just restart the daemon.