It's impossible to tell what's going on without seeing the details of your workflow and your timeline. Try selecting the layers in the time line that are giving you problems and then press the U key twice to reveal all modified properties. Make sure that the Composition Panel is set to Active Camera because that is the only view that will render. Check the settings for all problem layers to make sure they are not set to guide or adjustment layers. If you cannot figure out what is going on then post a detailed description of your workflow and take a screen shot of AE with the problem layers revealed, with the Comp selected in the Project Panel and a description of your render settings and workflow. Do not scale down the screenshot, just drag it into the reply field on this forum.