Files missing from exports

This is now getting ridiculous.  I'm on Windows 8.1 and have updated all of my Adobe products:  AE, Premier etc. to the very latest versions.
So this is happening:  when I go to export a composition, certain files within the composition don't make the final export.  It now happens so often with such regularity as to cause so many hours of lost work time.  I never had this problem until the updates.
For example:  working on a comp with many different elements, including some files from Videocopilot Element.  Half the time these Element files don't make the final export.  The exported file will have all of the other components EXCEPT the 3D files. This problem seems to occur more if I use the Media Encoder, which I am mostly forced to if I want the h.264 version.  If I use the built-in render machine, this does not seem to happen.
This also occurs if I import the AE file directly into my Premier project.
But, this similar thing is happening in Premier.  My last project gave me hell as certain audio segments would not export to the final project. [obscenity removed by moderator]
There are some serious issues going on with these new upgrades.  Please, Adobe, help us out.
Again, I never had any of these issues before the updates.

Does this issue of items not appearing in the final render happen with layers containing Element 3d only?
If not, what other kinds of effects are applied to layers that don't appear?
If it's just Element, I'd check for an update on VCP's end and/or file bug reports with their support team.
I'd suggest rendering to an intermediate codec and then bring that file into the Media Encoder to make your h.264 in the meantime.

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