Yep, I officially hate fillets, too. I ran into this exact problem a few months back with a model I was working with and posted my question here but got no responces at all I believe. I tried reworking the geometry, redoing the fillet several different ways, worked with the number of isoparms for each object, increased the tesselation, etc, etc, etc.... and to this day I still cannot figure out what the problem is, so I have given up.

for all I care, the fillet tool can go **** itself.