When you change the global desktop font size, the font size of the panel updates, but it does not resize itself accordingly. Therefore, the date still shows, but the time is cut off and completely invisible. It should either make itself wider to show everything, or do somethign else that I can't think of.
note: I'm using 18-pt fonts.
Seems to be working again now - I've a recollection of fixing it at some point. (The way it works is that the panel has a heuristic for the minimum size of the panel - enough to display a line of text with some padding on either side. Essentially, exactly what's needed for the clock. So, if the clock adds a pixel, it doesn't work anymore and we have to go back and either fix the clock or the heuristic. Sigh.)