I am working on a pretty big edit and having a problem with masks. When I preview the mask within AE, everything is ok, all is well, the sections that were taken out arn't there.
When I render, sections of the mask remain in front of objects that they were previously removed from.
It sounds as if you may be trying to use Open GL to accelerate rendering in AE. You shouldn't. Turn it off. leave it off.
If Open GL isn't the cause, it would be a great help to provide additional information, and you can find the list here:
If Dave's advise doesn't help, perhaps some screenshots would help to clarify matters. Sometimes combinations of effects with masks and features like inadvertently enabled collapse transformations or making your layer an adjustment layer can have funky results. You could also some how mess up your masking logic with layer modes like Stencil Alpha or using them as a matte... I'm sure there is some simple, logical reason for what you see.