It could be a bad drive. I've seen some drives that lose tracking at the outer edges of the disc. Both audio and CD-ROM.

But if it only happens on certain discs, check to see if it's a disc with an extra data-track at the end. I've had some discs confuse rippers because the ripper thinks the last song and the appended data track are the same thing. This usually produces the exact symptoms you describe.

The way around it is to edit the track length of the last track before ripping.