I have seen many I2C style interfaces that clearly specify a minimum clock (yeah, sounds odd, but..). Going slower has unspecified side effects. So that's an outside possibility, but the chip datasheet ought to have something to say about that.

Apart from a chip bug, the only other thing that comes to mind is EMI / spikes on the interface lines or mains power to the chip.

I'm sure you're poking at that stuff already, but there's only so many ways to get an RTC chip to mess up. It's got to be one of them.

Cheers