When you have an Adobe After Effects composition inside a Premiere Pro project, the changes you make to that composition within After Effects are not reflected in the output that is exported from Adobe Media Encoder.

Example: You create a comp in After Effects with some text. You place that comp in a Premiere Pro sequence. You change the color of the text in After Effects and then switch over to Premiere Pro without saving the After Effects comp. You see the color change updated in Premiere Pro, and then you export the sequence through Adobe Media Encoder. The changes are not shown in the Adobe Media Encoder output preview.

Solution: Save comp changes in After Effects or disable native sequence import in Adobe Media Encoder

Do one of the following:

• Save the changes to your After Effects composition in After Effects before you export your sequence through Adobe Media Encoder. 
• Deselect native sequence import in Adobe Media Encoder's Preferences: 
  Preferences>General>Premiere Pro>Import sequences natively