note that if you send directly to AME then it rendering and encoding one after the other so you should calculate your total render time of course for comparison (if you haven't already). even it total, it's actually sometimes a bit slower than rendering first, and then manually dragging the rendered file to AME but not by much.
if after reading this it's still an issue:
1. try resetting your AME preferences by holding shift as you launch it (there is no dialog screen)
2. under general preferences try to change the renderer and see if you get better performance CPU vs GPU
3. test a simple clean project with a few simple layers and see if this is the case too. isolate the problem as much as you can