[Matt Girvan]

To anyone who still has this problem, there is an easy solve:

Use Control-Click to select all of the layers in the area of your composition that has the problem. So basically, the part that gives you the error when you try and render or play it.
Right click one of the selected layers and choose pre-compose. Just click OK and you will see that the layers have been minimized into one composition inside of your composition. It looks neater and it works with the rest of your comp. Notice that it does not change length, so everything is in sync/time as before.