Having Rendering Issues - Help!

[mutually sharede47342772]

Hopefully a wonderful guru out there can help me. I created a video and it looks and plays fine in After Effects. However, when I render it (using Media Encoder as well as Render Queue) it is disregarding a layer or two. I have never had this happen before and of course I'm creating a sample video for a project at work. Any ideas on what this could be. Thanking you in advance. 

[Airweb_AE]

Aren't these guide layers?