Travis and I are doing back-to-back cruises in late summer of 2004. August 28th Western followed by the September 4th Eastern to San Juan. Haven't heard of any discounts for doing back-to-backs though.
Generally, even if they did offer a back-to-back discount, Disney won't "stack" discounts. For example, if you recieve a Florida Resident Rate you can't recieve an onboard booking credit for the same cruise. Or vice-versa. So, if they did offer a back-to-back discount, it may still be a better deal to accept onboard credits if that can be done.
Great question though!