My guess is that you didn’t choose Move All Attributes Into The New Composistion when you precomposed the layer with the effect.
Remember that the order of operations for non-vector layers is masks, effects, transformations. So in general a mask is not going to apply to the effects, because they come later. That’s why you need to precompose—to change the rendering order.
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Todd Kopriva, Adobe Systems Incorporated
putting the ‘T’ back in ‘RTFM’ : After Effects Help on the Web
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