Not all projects render at snail-speeds. Why?
Some of the frustrations of slow render speeds are often because they don't happen for every project. And then I discovered that the last few snail-speed renders have happened on projects that were started in previous After Effects versions... Specifically when compositions (from older versions) get nested inside other "new" compositions.
Food for thought—Hopefully this helps get Media Encoder and After Effects out of sick-bay.
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Jess McMillan (AE Dev @ Adobe) commented
Third party plugins that are not multithreaded safe can cause slower renders as one example. Have you tried using the layer profiler to see where your issues are? Is that how you tracked them down to nested compositions? Then in the nested composition are there specific layers/scenarios that stand out for you there or when you are rendering it not nested is it faster than when you simply include it in a new composition?
Thanks for your post and time in helping us investigate.
All the best,