Shape Layer Disappearing with Bottom Layer?

Quick background:

At my company we have used a standard open and close template on our product videos for years, this is an AE file. I typically import this template file into each new video and use the precomps built in that template. Since updating to  AE 2019 this file has been corrupted or something, it kept crashing my projects. So I rebuilt the project but now I am getting a similar problem.

Problem:

The template I use has a simple curtain reveal between two solid blue rectangles, the lower rectangle now seems to be linked to my bottom layer of the composition. If i remove the bottom layer the lower rectangle disappears. If I reduce the opacity to zero the lower rectangle disappears. Why is this happening?