1) Check that your files were analysed properly for the type of song; if the track has a consistent tempo from an electronic percussion, it should be analysed in NORMAL mode, but if the track has a live drummer with the potential for small variations in tempo, you should analyse it in DYNAMIC mode. If you use the wrong analysis mode, the song may be warped in such a way as to produce undesirable results.
2) Check that the beat grid is accurate. While the analysis is usually pretty good, sometimes it can be off, and thus if you think your tracks are in sync, it could simply mean the grids are in sync, but the audio is not.
3) Was the MP3 file a VBR (variable bitrate) file? If so, that could be a source of the problem with the compression having caused some irregularities in the consistency of the tempo.
4) Did you have Master Tempo enabled with a large pitch percentage? Sometimes the large variation in tempo from the origin with MT enabled can cause some audio artefacting, which leads to it sounding like it's out of sync.