I had an urge to check my XDs when I read the first post, at work.
Whoops, hehe. Yeah, let's keep that out of sight around other people...
So, when I got home and changed into my workout clothes, I unstrapped the XDs, cleared it, and checked - my barrel rides low in the slide as well. As noted above, the slide opening is larger than the exterior of the barrel, because as the slide moves, the barrel moves up and down.
Clear your pistol. Check it visually and digitally (stick a finger in the chamber to verify that it's empty). Then, run the slide back and forth by hand as slowly as the spring will allow you to, and you'll see the barrel rise and fall as the slide moves.
As for shooting low...are you flinching/anticipating the recoil? Have someone observe you while you shoot, and see if you're flinching, which would be evident in a muzzle-dip right before the bang. Or, do you need to adjust your grip and sight picture? With my XDs, I went through a phase where I was flinching. I adjusted my grip, and my attitude, and she's dead-on-target now. More accurate than I am, anyway...