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not the best answer but have you considered updating your OS? I've had this issue in the past but not since updating my Operating System to 10.12 and later.
another work around might be to just render a higher quality format (prores/cineform/animation/etc.) and drag those into encoder. it adds a step but that step will for sure be way less time than waiting for a laggy link between apps. furthermore, you could set up AE to render to a Media Encoder watch folder and save yourself the effort of dragging the lossless renders over.
I've had comps for render that never show in Media Encoder too. It doesn't appear in any way to do with the size, at least in my experience. Sometimes, it just doesn't show.
In each case, all I've done is shut things down, reopen the project and try again and it works. Maybe empty cache along the way.
It's never created too much issue for me to do that though.
80MB for an AE project file is huge, that's why it takes a while. AME files will take a bit to show up but if they're failing then clear your image cache and see if that improves anything, and make sure you aren't running any other programmes or apps.
Cheers, The watch folder idea is a good call.
I have updated my OS many times over the past 2-3 years and repeatedly come accross this issue on multiple machines. Currently the new OSX (Sierra) is causing problems on our network so I am holding off on upgrading this machine's OS.
I usually render files of this size straight from Ae in Prores, as per your suggestion, but sometimes I want to cue renders from multiple projects or keep After effects free to make small edits to other jobs while rendering.