That's very odd. I've not seen anything like that before.
Does RTC hang at the point you press "S" to set the time or does it continue to function until you select exit?
If it hangs at "S" then it sounds like a fault with the data or write signal to the DS1302, but I can't think how that would cause it to fail as described.
Another possibility is it writes to the DS1302 in such a way that RomWBW somehow hangs when reading from it - seems unlikely.
I can't think of any really likely scenarios.
Perhaps you could post the terminal output showing RomWBW starting, the RTC being set, and the RomWBW failing to start afterwards. Perhaps there will be a clue there.
I'll think some more.
Steve