I'm still not clear. The Only Layers that appear layers is confusing me. If you turn them all off what do you see in the composition window? Do you want to see more?
Usually the first thing to do when troubleshooting a problem with After Effects is to PURGE all memory by going to Edit>Purge>All Image and Disk Caches. If that does not solve the problem then I would turn off MP rendering if it is enabled. If that does not solve the problem try turning off one layer at a time until you get something to work. Then turn that layer back on and start turning off any effects that have been applied to that layer.
I really am trying to figure out how your composition is made. A flow chart would help me see the structure. I get a little clue from your After screenshot because it shows three frames rendered. What does frame 1 and 2 look like? What does your composition look like when the current time indicator is at frame 3? One more idea. Turn off every layer that is not part of the design. It looks like only the layers marked "Only layers that appear" are the only layers you need in your composition. If that is true, turn off or delete all of the other layers.