Hi Branden, ok now I think I see a little more clearly where the problem area is - it is related to the sharp angles, the corner patch over in this area is twisting awkwardly:





In this particular case it's able to build that result better though if you extract just those faces into their own separate object that is not a solid, like in the attached file. In this version you should be able to make a complete selection like this:



Then it will make the fillets but if you zoom in to those corner areas shown above you'll see those corners are malformed and strangely swoopy so it needs some tweaking in those areas but the other areas seem to be ok.

EDIT: forgot to attach 3DM file, attached now.

- Michael