Yes, the NavMesh is still not baking quite how I'd like. Though I believe I did fix the level building on top of itself. There were many kinks I had to discover and work out regarding building a game that uses procedural level generation... I had no idea when I started it would be this much of a problem. The build creating process has been much more involved this time around.
I invite you to try the downloadable version if you haven't already and see if it is any more stable. Thank you so much for playing!