This is due to the focusing screen, which is a small piece of etched glass above the mirror and below the pentaprism/pentamirror, is misaligned. I've had this problem a couple times with my 450D, as I've had to take my focusing screen out on a couple occasions to clean it due to some thing getting thoroughly stuck on it. After reinserting the screen, my bottom AF point on both occasions ended up exactly how you described. Sometimes the AF point will look a bit shadowed, and show a bit of a glow near the top, when alignment is particularly off.
It can take a few tries to get the screen reseated properly such that it aligns correctly with the AF point lighting apparatus. If you removed and reinserted the focusing screen, this can sometimes be due to stacking the filler plates incorrectly...they are fairly precisely machined, and should be paired exactly how they were when you first bought the camera for perfect alignment.
If you are not up to realigning the screen yourself, you can probably find a local shop that could take care of it professionally. It should be noted that a misalignment will not have any effect on your pictures themselves, as the AF point highlighting is a physical aspect of the viewfinder. It will only be an annoyance when the lights blink, but otherwise is harmless.