My NavMesh is baking way above the Terrain/Objects

So I'm experiencing A very strange issue with my NavMesh, it is baking way above the Scene in the middle of the air. At an earlier stage in the map it was baking perfectly fine onto the Objects/Terrain, since then I added a lot more objects, and used the Mesh Combine Wizard to merge some meshes together, I then rebaked the Nav Mesh and now it will not Bake onto the objects, but instead Bakes way above the Objects, in the Air. This is not limited to the Mesh that I combined together, if I place a Cube and rebake the NavMesh, it will still bake into the air.. I have Mesh Colliders on most objects, changing the Colliders does not seem to affect it. I have made plenty of other Maps and I have never encountered this before, I have asked multiple people and they also have never seen or encounted this before. I tried adjusting the Voxel size, the Baked Agent size and other Navigation settings but to no avail. Im really stuck and i'm not sure where to go from here, I would love to not have to scrap this map. :/

Any help or suggestions will be greatly appreciated. Pics below.

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[1]: /storage/temp/162862-navmesh4.png