I'm having a devil of a time editing out unwanted silence at the end of mp3 tracks
bounced from a Logic sequence. I find that if the end point of the bounce is too close to
the end of the audio, there occurs an echo/spike that ruins the silence at the end of the
track. This happens even if the audio has reached a silent state. it all depends on how
much time is allowed between the end of sound and the bounce end point.
If you are importing the MP3s into Itunes, you can adjust the start and end there (for example, I might cut of a few seconds of intro by starting at 0:06 (6 seconds in)).
You might also try bouncing to AIFF and see if you get the same echo, and try to bouncing real time ... there have been reports of problems with offline bouncing.
What might be happening is that Logic loops around, so when you get to the end of the loop for the bounce is might load the buffer with the start of measure 1. I have had the experience of hitting PLAY and hearing a click or glitch in the beginning (where there should be silence) because logic is holding over something in a buffer from the last play.