To be honest, it’s really hard to tell what’s going on from the limited screen shots and your description.
Looking at the settings, it looks like you are trying to use effects to fill in the background, so that the text is all one layer.
But you’ve use Set Channels to achieve this, I would use Shift Channels instead. Set Channel is filling the dimensions of the precomp (at least that’s what’s happening when i try to recreate your set up). Shift Channels with Take Alpha From set to Full On should get you the result you’re after.