Sounds like a graphics issue; I can't imagine anything more useless than a crosshair that you cannot see through.
Andn you can check if it affects rebel ships or not by playing a skirmish game and flying an X-Wing. Or a TIE Fighter for that matter.
You know, I AM tempted to re-install this game now...
Bumping this one again...
I finally have x-wing alliance reinstalled, version 2.02 and I STILL have the same problem with the shooting practice (and it's really strange because I finised the game once and then suddenly I have those problems)
I'll see what the "official" guys say about this, but if anyone has the game and knows what's wrong, let me know!