AE and Media Encoder 2018 problem generating a GIF

Your workflow is almost completely wrong. You are treating animated gifs like they are movies and they are not. Here is the most efficient way to create an animated gif using After Effects.

The first step in efficiently creating an animated gif is to figure out exactly how many frames you need. Let's say that you have a slideshow with 20 slides, so without any time for transitions, you need 20 frames. That is all, just 20 frames even if you want your animated gif to last for 20 minutes because you can tell the software you should be using to create animated gifs how long you want each frame to stay on the screen and every single frame can have a different duration. Now let's say that you want to have a 20 frame transition between slide 1 and 2 and slide 10 and 11 and all of the other transitions are just 4 frame fast wipes. Let's do the math. Twenty frames for the slides, two transitions at 20 frames each, so that is 40 more frames. We are up to a comp that is 60 frames long. Now we have 18 transitions that are 4 frames long so that is 72 more frames for those transitions. The total comp length needs to be 132 frames. You now build your comp with just 1 frame between each transition.

This is completely different than you would build a video, but you are still working in After Effects. You don't care about the timing of the preview because you are going to fix that timing in Photoshop. You now render your composition using the Render Cue to a lossless video format using the default lossless template in the output module.

Next step, open the rendered movie in Photoshop, open up the timeline panel, start selecting frames and set the duration of each frame inside Photoshop. Slide 1, the first image, you want to have on screen for 10 seconds so you set the duration of frame one to ten seconds. The next 20 frames in the Photoshop timeline are a transition between slide one and slide two. You want that transition to take a half second so you set the duration of each frame is 1/40 of a second so you set the duration of those 20 frames to .025 by selecting all 20 of them and setting the duration. Then frame 23, which is slide 2 is set to 10 seconds. You repeat for all of the frames in the timeline and you then export your animated gif using Photoshop's export for web feature.

Here are the advantages over creating an animated gif like you would create a movie. One, A HUGE reduction in file size. In this case, the file size would be several hundred times smaller than if you created a 15 fps movie for the whole slideshow and exported an animated gif. Second, and probably even more important, a tremendous increase in the dithering and color conversion from eight bits per channel (millions of colors) to the 256 colors that are available in the GIF format. That's all of the color values you can have - 256.

That's how you create the best quality animated gifs using After Effects. There is no other workflow using AE that is as efficient. The only other option for creating efficient and good looking animated GIF's is to use a program specifically designed for creating them. Any good animated gif software will be doing what this workflow does under the hood. You should never have an animated gif that has two adjacent identical frames because the Animated GIF is the only "movie" format that lets you set different durations for each frame.  You can do it in HTML 5, JavaScript, using Flash (Adobe Animate) and other programming languages, but you can't do it in any other movie format.

If you insist on seeing your preview in AE in real time then you can still export a lossless movie in After Effects and use Photoshop to export the animated gif but you should take the time to go in and delete all of the identical frames and set the timing of the remaining ones in Photoshop. You should also limit the frame rate to no more than 15 fps.