Hi Skwerm, were you able to get your piece finished up how you need?

Something in the filleting system seems to be getting pretty confused in your original case. One way to get it done still is to use the "lower level" surface/surface filleting which can be done between 2 separated surfaces. It can give a fillet surface result in cases where the edge based one gets messed up.

I've attached a model where I constructed a pocket that way - I did a boolean with your piece (I rotated the spheres around so that everything had their seams in one side), then did a boolean to cut, but then to do the fillets I used Edit > Separate on the model to break it into individual surfaces and selected 2 surfaces at a time and then did a Fillet. The surface/surface fillet that was then generated can be used.

To finish it you would need to array the current filleted fragment (which is sunken down into the main object now) around again, then use Edit > Trim to trim the main object by the set of fillet pieces, then join the pieces together. This kind of low level surfacing approach (using surface/surface fillet and trimming) is not as convenient as booelans and edge-based fillets but it can get the job done when the regular filleter is being cranky about something.

- Michael