Although it doesn’t happen all the time, I’ve run into two cases where the mp3 file created in Cubase has different endings and content when used in other players. In one case both QuickTime and SoundTrack Pro showed the lengths approximately twice as long as the Cubase project with silence at the end. In another case both QuickTime and SoundTrack Pro reported the same lengths. However, whereas SoundTrack Pro showed a duplication of the audio in the Cubase project, QuickTime had only a few seconds of additional audio.
I have had no similar problems when I export these projects as wave files. When I import the bad mp3 files back into Cubase, Cubase interprets the file to be the same length and content as the project. The only solution I have found so far is to completely recreate the Cubase project. In both cases I had used the same Cubase projects for previous songs but had cleared the prior content and used the project as a template.