Your most likely problem is workflow and user error. Are you new to AE? Did you modify any of the Render Cue settings like Output Module or Render settings? Did yo use the Adobe Media Encoder to render? Did you modify any of those settings? Did you check the render details by either importing the footage into After Effects and checking the file interpretation by selecting the footage in the Project Panel and checking the info right of the thumbnail preview at the top of the Project Panel? Did you check the file Interpretation in Premiere Pro? Did you create a custom composition in AE?
Check the settings? Check the rendered file. Unless you know exactly what you are doing you should always use the presets that come with After Effects for Composition Settings, Output Module and Render Settings. You should not see Custom in any setting description. If you use the Adobe Media Encoder you should also use the presets and they should match your comp settings and frame rate.
To learn about rendering and export type rendering or Expert in the Search Help field at the top right corner of After Effects and check out the community resources. Video is very complicated and you must understand the standards for frame size, frame rate, and compression before you monkey with the settings or you will end up with problems.
Thanks for your input. I am not new to AE, but not an expert by an means. The only change I made to the render cue was changing RGB to RGB + Alpha so the transparency would render out as well. Other than that, everything still remained as default settings. I did not try Encoder, I will give that a shot a see how that works.
Did you use the lossless with alpha preset?