I just noticed that the regular activity heatmap doesn't show the rest symbol on the days that were holidays, whereas the schedule-based heatmap (I forget exactly what it's called) does show it. Not a big deal at all, of course, but I'm guessing it's not typical.
I do see them showing up on both versions of mine. Do you mind sharing some screenshots of what you see for both versions of your heatmap? That'll help me in seeing what's going on.