If you are getting the darker band, then you must be using a shift device such as the zoerk? or other. Or just a normal shift lens?
If so, when you shoot, you need to make sure you have enough overlap to cover the darker area of the image. Also if using a 5D, not sure how it reads WB, but if it's like the 1ds MKII MKIII, then as you shift and reduce the light, the WB reading will change. This will make it very hard for any tool to automatically stitch the images due to the color changes. The 1ds MKII reads the WB off the sensor, no external reading, so I always manually set the WB, this way all the image shot will be the same WB.
The use of a shift lens, or zoerk adapter will leave the darker band, and the more you shift the more the inside edge will be dark. For the work I do, I will most times just manually stitch the images together in CS, but as was previously posted, if you have a large number, of image, its best to use software, CS3's or autopan, or panotool, or stitcher. Most will put together a good image. However many of these tools will get confused if you have the darker area, on one side of the image and try to merge that, which will not result in a good image.
Paul C