Quoted from docquest:
I then used the “Photomerge” feature in Photoshop to automatically stitch the separate scans into one continuous image. It took a few attempts to get it right. I found out that if the individual scans are skewed too much then Photoshop has a tougher job aligning them back together accurately
I've found photoshop (at least CS2) does a pretty terrible job at photomerging. If you process it through microsoft's ICE (free) it does a much better job of aligning them.