I am not aware of After Effects being certified for that use, so I am actually surprised that you have it working at all
John, you can build little AE render farms. It's a bit more complicated than Team Render with C4D though.
Juliee, what version of AE is running on each node?
I don't have any other suggestions off the top of my head. You might consider contacting Adobe support to see if they can help.
We had the same issue in the last couple of days. Currently we think we might have figured out a workaround. Our "ae_render_only_node.txt" is in the "USER\My Documents" folder and apparently it was a problem that we were previously logged in to CC as normal user to install some plugins etc.. The fix now is to simply make sure to be logged out of CC on all machines before creating the ae_render_only_node.txt:
1. Delete the existing "ae_render_only_node.txt"
2. Start After Effects with the GUI
3. Help->Sign Out
4. Create the "ae_render_only_node.txt" in the "C:\Users\[USERNAME]\My Documents" folder
5. Use a different user to actually work in After Effects
I hope that helps you as well.