Sometimes when you drag a file into Adobe Media Encoder you'll see an error "File Import Error" and something about "Could not read from source".
This usually happens with .mov files for some reason. I'm not sure why, but to solve it temporarily I've just been renaming .mov files by appending .mp4 at the end. These files are in fact .mp4 files but for some reason Adobe Media Encoder seems to get confused if they're named .mov. Go figure.
If you change it to something and it still won't import...I have no idea.
This link from Adobe offers a little more information. Even they admit it's a confusing mess:
"The codecs that are found in Adobe Media Encoder depend on which version of Creative Suite or standalone program that is installed. So, while a codec might be installed in one version of Adobe Media Encoder, it might not be found in another."