Burning CDs from iTunes
That is odd. The only thing I can think of is that perhaps the start/stop times of some individual songs have been changed. Try this


Find a song that this happened to
Get Info on it (right click on the song in iTunes and select Get Info)
Click the "options" tab near the top of the Get Info window
Check and see if the start and stop times have been changed. Start should be "0:00" and end should be the full length of the song in minutes and seconds.


If those times are set incorrectly the songs will be clipped/truncated when playing, creating an AAC version of the song or burning to CD.

If that is not it... well sorry I don't know