Hi TpwUK!

Fillets can be tricky for the program to work around funny seams and the complexities of angled surfaces.

You can see here how I tackled a model's inability to fillet in particular areas by fitting customized Blends:


Please see my tutorial to get a better idea on how to use Blends to solve problems that auto-Fillet cannot:


http://moi3d.com/forum/index.php?webtag=MOI&msg=4607.5


You'll use an intersected representative curve to sweep a circle on. You'll subtract the swept object from your surfaces, deleting the un-needed material. Then you'll use Blend to painstakingly patch small sections of edges together to form a custom fillet. Of course, you also have to manage the edge curves by adding trim points and using the "Merge" command to join segmented edge curves together that are not separated by an intersection.

I hope that you are able to understand what I am talking about. It's just a complex fix around an often too-present problem.