Rendered output is acting strange

[Ridley Walker]

Are the layers 3D?

If so and they are on the same plane try moving the background 1 or 2 pixels back on the Z axis.

[Johnny Harris]

That actually didn’t work for me. Yes all layers are 3d.

[Ridley Walker]

The glitch you’re seeing looks like the typical interference intersection of 3D layers on the Z axis. After Effects has problems when multiple 3D layers are in the same Z position, separating them by a few pixels usually solves the issue.

OR

Are you in CS6 and using the Ray Traced Renderer? If so try switching to Classic 3D.