Well, damn. Been a while since I've seen the episode. Maybe they just forgot about the day they shot the Jack Crusher hologram scene?
The best in universe explanation I can think of is Jack dressed hurriedly to make the recording for Wesley. Fathers to be don't get much sleep, Starfleet officers probably even less. Or else the recording isn't 100 percent compatible with the latest Holodeck firmware, and some bits are missing?
Why do you keep picturing Jack Crusher naked? ;)