Premiere / Media Encoder exporting corrupted video clips

So I have a number of premiere sequences each with a group of 2-3 clips all of which were rendered in quicktime. Some using Animation as a codec and other as Animation w/Alpha.

All of these clips were rendered out of After Effects.

I used premiere to sequence in audio clips and sound effects and needed to export them out as Quicktime Animation.

Upon playback on my VLC..the clips start fine then 3-4 seconds in a whole bunch of video noise fills the screen. The audio still plays til the end, but visually its all video noise.

I tried exporting these from AME and the same thing occured. I did try to change the settings on the export from quicktime animaion 8-bpc to 8-bpc+alpha. and it reversed the noise...where the video starts in noise and then 3-4 seconds in it plays the video correctly.

This was nerve-wrecking as the device these clips are made for only accept Animation codec and not the more common ones (like h.264)

I finally found a work around by copying my sequence from premiere and pasting it in an empty composition in AE and rendered them out from AE again...

The video played out perfectly.

So is there something I am doing wrong or is Premiere running into a limitation when it comes to Quicktime Animtation that the AME also has yet AE doesnt?

I am running this on a HP Z820 / Xeon E-2625 / 32 GB RAM / Running Windows 7 SP 1..  Premiere Pro CC 2017, AME CC 17, and AE CC 17..all with latest updates.