Hi amyanne,
This is strange. One possibility that comes to mind is that the CD burning software you are using adds silence at the end of mp3s when it decodes them. I'm assuming here that you're burning to an audio CD, rather than a data CD with mp3s on it? If that's the case, you could try opening the file in WavePad, editing out any dead time, and then saving as a .wav rather than .mp3. Then burn the .wav to your audio CD.
In general, working with mp3s is a hairy business. They make a lot of compromises in sound quality, and different encoders and decoders will result in different file lengths because they add varying amounts of silence to the start and end of the files when they encode or decode them. If you want accuracy, work in a lossless format such as .wav.
Alex