I've never had good quality h264 straight out of AE so I guess I'm used to rendering high quality from there and creating the smaller proofs in media encoder.
Silly question but is 'Use Maximum Render Quality' checked?
It is indeed, yes.
What happens if you render an intermediate file out of AE first and then use the Adobe Media Encoder on that file? Does the result look okay?
It may have something to do with the content of that composition too. On that same project, you could try rendering it in CS6. You can Save As CC from CC 2015.3, CC 2015, or CC 2014 and then open it in CC and save it as CS6. (CS6 and all later versions of AE are included in your CC subscription and can be downloaded and installed alongside each other. Details on how to download here.)
If I do a high res intermediate then it looks fine, whether out of AE or MC.
I didn't realise that CS6 came included with the subscription. While it probably wouldn't be a great option in this instance, it's good to know for other situations that I've encountered. Thanks!
I've just tested it out some more and noticed that that low-res proofs causing the problem all encode much faster than a high res version in MC. I'm guessing from this that MC auto adapts the Resolution based on the export size you've selected? In After Effects this is an option under Render Settings, but it doesn't seem to be available in MC. Can anyone confirm if this is the case?