You have a setting wrong in Audacity. Even when the right settings are checked, Audacity will add a bit of silence on the end of the .wav, a real pain if you want to convert several 24/48 .wav's to CD quality without combining the tracks first and then re-tracking the whole show. This is a much better, higher quality, free sample rate converter, adds no silence, and will convert bit depths with dithering as well if you need that:
http://www.voxengo.com/product/r8brain/