I made it happen again! But it's not the second row of locations like I thought, it's actually connected to another issue I reported in a separate comment - the side girls appearing on top of the dialogue box! I think their paper dolls (or whatever) aren't scaling correctly, and I the added height of some of them is what is causing the clock to disappear.
And now that I can replicate it, I should also note that advancing to a new time block does NOT always make the clock return. :/