I have an AE (version 15.1.2) composition containing imported PS layers (yes, I imported them correctly as layers, not footage) and shape layers. The comp is rather large (10k x 10k). In it, I have a PS layer containing squares of different colors, each is a little under 8 x 8 pixels. The whole canvas is covered with these squares so there are more than a million. It's a video that gives a graphical representation of just how immense a million is. I start with one large square, then 10 and 100 and so on until I have more than a million.
When I attempt to export to AME (version 12.1.2), it seems to render fine. I am using H.264, Match Source, High Bitrate. The end result only has audio when I attempt to play it in Windows Media Player or VLC. Ironically, importing the rendered video into my project and placing it into a comp, part of it shows up at the beginning of the video (when I have only one square). I've even tried rendering at a smaller size output, to no avail.
-try rendering directly out of AE
-try rendering video only out of AME
-try rendering a smaller low rez movie out of AME
-in other words, change up what you're doing to see if you get the same, or different, behavior
If all else fails, quit all programs, restart the machine, try it again.