Your issue is that in your original curve creation, there is a hard point located in the curve, that creates a seam edge in the extrusion, then your next cutting curve, is just "skimming" right along that seam edge at something like .001, which makes the tiny surface that kills the fillet.

So here if you run seperate on your original cutting curve, you will see this point here...(Thats why the rebuild makes it work, as you can remove this seam edge)



So if you extrude that middle surface before you cut the ends off, you will see this seam in the extrude (note the second cutter above)



Then when you slice with that second cutter, you create this little surface here, that kills the fillet.