This question has already an accepted answer, but I'd like to give my two cent. We made i-net PDFC that perfectly matches your scenario. It has been made to check reports made with another reporting tool match the output of our reporting software. But its even more powerful. What PDFC does not do is: check image-based pixel perfectness, but it checks, with certain settings, that a document is basically (and visually) the same based on its content. Way more powerful than pure pixel-based comparison.
i-net PDFC can operate visually or command-line based (e.g. to batch process) and works with continuos integration systems. The visual component even allows semitransparent overlaying the two PDF files to have the user check the pixel-perfectnes.
The software is fresh out of beta. Give it a try and let us know what you think. (Yep. I work for the company who made this.)
