Is my understanding of D-Flip Flop wrong?
What you're running into here is a quirk of Logisim. Each simulator "tick" is resulting in half of a clock cycle, not a whole cycle. (You can see this in the screenshots: the clock input goes from dark green to light green after the first tick, and back to dark after the second tick.)

Since the D flip-flop is set to trigger on the falling edge of the clock, the output only updates after the second tick because that tick is the one in which the falling edge occurs.

Hooking the clock input up to another digital input (like you've got for "load" and "in") may make it easier to play around with this circuit.