Steve-
I don't know what fillet material you used, but here's what I do. My fillets are either balsa or epoxy with microballoons. They are applied over the silkspan or other covering. I sand them to the desired radius with medium abrasive (< 300) to remove residue and so that they are smooth, but rough enough for give added surface area for adhesion. Then I paint the butyrate on with a brush, first at both edges, but not along the center. When that is dry, I run some down the center. I do this in thin coats until time to spray silver. The spray is thin. That doesnt take much time, but I've never had any bubble or otherwise lift. If you sand or use solvent to remove whatever has bubbled, you might try this technique that doesn't allow much shrinkage area at any one time across the fillet's width. The photo is of a tail fillet, but the larger (R=1/4") wing filets on two planes look about the same.
SK