I have a repetitive problem with sending composition from the After Effects to render in Media Encoder: the composition contains existent and valid media, while once it's in ME — it shows a 'color table' of missing media. I started to get this problem over and over again on multiple projects.
Watch attached file with screen recording showing what I mean in a demo flow.
I'm using ME 15.4 and AE 18.4.0 on MacBook Pro with macOS 11.5
You are scrubbing the timeline while looking at the Footage Panel in After Effects, not the Composition Panel. This gives you no clue as to what is going on in the composition. It looks like nothing is going on. There is also no indication of where the image file sequence is located. What happens if you drag the image sequence directly into the Media Encoder? Where is the image sequence located on your system. You have not given us much to work with. I'm still on 11.4 and am having no problems.