Hello jessekirbs,
From what you describe you have many assets that have been imported into UE4 from Maya. In UE4 you are controlling the animation that was made in Maya by way of Matinee. All of your assets work fine except for two. These two are visible in your editor but not when you press play.
I have a few questions for you.
1.) Can you create this in a fresh project?
2.) Does this happen when you create a project with this animation and objects in 4.9?
3.) Can you link me a screenshot or YouTube with this happening?
If you would link me your DxDiag along with the rest of this information then I will continue to investigate this problem at that time.
Thank you,