I don't know how related this is and i wasn't able to test it but i got a large number of tracks cut off from some CDs. I found out that it was most likely the CD burner i was using as when i switched to a new reader, the problem disappeared. The probs you are having may be reader related.
Sometimes it may be a small variation in the wav file that throws the encoder off. Unfortunately for me this only really happened at the end of some CDs, after a particularly long ripping session and i didn't find out until the party i was playing them at.

Murray 06000047
I don't think, therefore I am not.