Hi krass - I'm not entirely sure but I think that the problem might be a very slight (like maybe just 1 or 2 degrees) tangent difference between some of the large pieces. Even just a slightly sharp area means that fillets do not naturally have their ends aligned. When I do surface/surface filleting on those the fillet ends are just slightly off from each other and that usually should only happen on slightly creased things.

Either that or maybe some bug in filleting related to handling fillets that cross over the seam edge of a closed surface.

- Michael