Hello Mungen87,
Thank you for the clarification,
I seem to have found some more information about my problem and have been able to narrow it down to the render order.
I made a video to summarize my issues: three render order issue - YouTube
Basically, depending on the order at which I load in my instances, it will cause either the red or the blue slices to render correctly. If I load all of the blue instances on the screen, set the opacity to zero, then do the same with the red, the blue will work while the red will not (vice versa).