To Many Mattes cancel each other... Maybe?

I'm still not exactly clear what you are doing. As per your flow chart you are not using any effective matting or at least not in a place where it would matter and do something. If you really want them to have any relevance they would have to be much higher upstream. The most obvious flaw in your chart is that your wave motion is actually only linked to one of your comps, so maybe you need to duplicate it and insert it into the otehr comp. I also can't see the solid you mentioned anywhere, so yes, something is most definitely not set up the right way.

Mylenium

Agree with Rick. Your screenshots tell us nothing because you cropped them and they also don't show any native matting being used anywhere nor any effects such as Set Matte. It's really impossible to make sense of what you are actually doing. Some full screen screenshots of all the comps with the relevant properties exposed would certainly help.

Mylenium

A flow chart would be helpful. I don't see any Track Mattes on any of the layers in any of your screenshots. I don't know how you are generating mattes. I don't see any animated properties on any layers. I am not sure that I can be of much help without a lot better understanding of how you are using the mattes.

When I have something complicated like you are describing I try and either create animated reveals using a track matte for a single layer or using Set Matte on a bunch of layers. If you apply a matte to a layer it should create transparency on that layer and no other layer. You can have multiple instances of Set Matte set to invert matte, all pointing to different source layers that may or may not be turned on (visible) to poke multiple holes in a single layer or if you add Invert/Invert Alpha at the bottom, you can reveal different parts of the layer. Soething like this:

It would really help if I knew what was going on in the comp. Here's the flow chart for this example: