Thank you so much for your help! I've been banging my head against these problems for days, and other forums have been pretty unhelpful. I will give those fixes a try.
So I just realized that Ihad the control set to Direct instead of Point and Click. Upon changing it back, the Navmesh is now working correctly. Is there a way to make it work with Direct Control? I find it much more preferable than Point and Click.
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So I tried dropping the 2D demo character in and it still isn't working correctly. Both Unity and AC are up to date.
The sprite and backgrounds are both very low-res, as I'm trying for a very grimy Gameboy-esque style. I have to scale both of them…