I had this same issue and may have found the issue: a corrupt Media Cache / Media Database. I closed AE, went to my library manually deleted my media cache & database folders via Finder (I didn't use the cleaner buttons in AE's preferences), emptied the trash. After this, I re-imported the problem files and they showed as video files. Hopefully this works for everyone else as well. ... View more

If people are using LUTs applied via Lumetri in Premiere and then having issues upon export in Media Encoder, I think Takuya's suggestion is the first thing they should check out. That was the issue when I had a discrepency between Premiere and Media encoder. In my case I was using non-Adobe Canon camera LUT that I downloaded myself. This LUT was in Premiere's Lumetri>LUT>Technical folder but not in the corresponding folder for Media Encoder. The resulting export looked like the software just randomly selected another LUT that came standard with the install when it couldn't find the one from Premiere and the footage became oversaturated as a result. Also, the same rule applies for After Effects! It has it's own Lumetri LUT folder in the same location inside the AE application folder. You need to copy your LUTs to that folder as well otherwise dynamically linked files from Premiere that have Lumetri with a LUT applied will have the same issue. ... View more