It can come from both. Lets pretend the five lines represent how far off the mark they are.
This would be perfect
body .-----.
lens .-----.
This would be a little off, but close enough to go out the door of the factory and sold. If you get a body that back focuses and a lens that front focuses the same increment...they can cancel eachother out.
body -.----. (the DOF will be closer than it should be)
lens .----.- (the DOF will be farther away than it should be)
They are both off, but opposite directions, resulting in a perfect result.
You may get something like
body -.----.
lens -.----.
Instead of canceling eachother out, they both contribute to the problem and amplify the effects.
This may (or not) be what is happening to the OP. The body and lens are both front focusing. One is front focusing way out of spec and really causing a ruckus.
body .----.-
lens .--.---
It should be noted that this condition would be extremely rare and unlikely. Many people go way overboard thinking their equipment is out of spec when in reality, it isn't.
The new cameras, such as the 50D, have an adjustment to correct for minor front and back focusing. Lets say your quiver of lenses looks something like this. You can tell the body to back focus or front focus on purpose, compensating for the lens! The body will remember the lenses and automatically use your configurations with each.
lens .----.- body -.---.
lens -.----. body .----.-
lens .---.-- body --.---.
The OP's XSi does not have this feature, so if this is the problem, he can send his stuff to Canon. If he sends just the lens, they will correct it to spec. -.----., .-----., and .----.- are all considered in spec. If the lens is .----.- off, they won't do anything and just send it back because while the lens may not be PERFECT, technically there isn't anything wrong with it.
If Canon sends just the body, they will correct for that but the lens could still be way off. If the OP sends both body and lens, they will change both to work perfectly together. Canon got tired of receiving entire quivers of 10 lenses and multiple cameras, so they gave us the power as long as the difference is marginal. If I have a .--.--- lens I would still send it in though.
**It should be noted that this illustration is 100% improve. I have never seen this information presented this way and I am not striving for technical accuracy...just explaining the core principles on their most basic level.
