Trying to add multiple text layers to Element 3D

You cannot have more inputs than what the plug-in offers but you can try and add a second instance of E3D and enable the unified renderer. Depending on your hardware this may not work, though, and quite general what you are trying to do like it is simply beyond what E3D ever was designed for.

Mylenium

There is no way of telling what you have done wrong without seeing screenshots of your comp, your Element setup, and having a detailed description of your workflow and setup. We need to see the modified properties of the problem layer. 

I suspect the problem began with the initial setup. I don't have time to show you how I would do it right now, but you should be able to get some hints by going to Video Copilot and looking at their well-produced and explained tutorials.