I've had some chiropracters out and they have helped but the best thing I ever did was to get this horse massuese (sp?) out. She is really, really good and knows so many techniques and she has made a huge, huge difference with one of my old horses in particular. Although, there are a lot of horse massaging people out there who aren't overly great but one thing this woman told me was that even once you get the back put back in with the chiropracter that if the muscles are damaged a bit, as they often are after a slip in the paddock or such, then even though the bones are fixed the muscles often pull them back into the previous state.
I would recommend the chiropractor, but remember to look into how your saddle fits. It may sit right but each horses back contour is different, which means unless you have had your saddle exactly restuffed for your horse then chances are there will be some unfitting parts of the panel, and one of these could be causing a problem. If it is something like that and you fix the horses back then saddle could just hurt it all over again.