Try making a CD with a bunch of short tracks and see what happens. If its a mechanical problem with the transport, the problem should start when the laser moves out to a certain distance. The track number shouldn't matter.
Next, play a few songs and don't stop until the problem occurs. (or in this case, goes away). Lets say it takes 5 tracks for this to happen. Now play the CD with the short songs on it. If you get the same result of 5 tracks, the problem may lie elsewhere because the laser isn't moving the same distance as it did with the first 5 songs. If the issue is mechanical, you would need to play more than 5 of the short songs to get the same distance.
Next, play a few songs and don't stop until the problem occurs. (or in this case, goes away). Lets say it takes 5 tracks for this to happen. Now play the CD with the short songs on it. If you get the same result of 5 tracks, the problem may lie elsewhere because the laser isn't moving the same distance as it did with the first 5 songs. If the issue is mechanical, you would need to play more than 5 of the short songs to get the same distance.