Media Encoder dropping Audio

Hello, this is my first time posting on here, but I need some help.

I am editing a video between Premiere and After Effects (both are the latest versions), my export settings for both are a "custom" Apple Pro Res 422 HQ format and the playback, after being rendered (in the Render Queue), plays with no problems.

I then take my videos into Media Encoder, with a "custom" H.264 preset (CBR is at 50). The playback once the videos are finished, cuts off the last 2 seconds of my audio. 

I am not dealing with any video problems with the encoding, just audio. I have tried looking for a solution and haven't been able to find one that works.