That's a strange one. Where is the audio lost from? Is it just silence at the start or end of the tracks, or is audio lost? What are you using to join the tracks? It can be done with Batch Join, or simply by copying all of one track and pasting it into the start or end of another. Finally, is there anything different about the files which don't join properly? Is one stereo and the other mono, for example, or do they have different sample rates?