I have been having a problem here and there with the fillet tool...

I managed to fix your problem.... workaround, not fixed.
1. from the top view, draw a straight line that can be used
to boolean cut a sliver off your 2 extending squaure pieces.
2. select the edges that make up the now open square and use the
planar tool to create a new piece.
3. use the join tool to attach the new planar sqaure sheet and round away.

I hope I wrote that clearly...

Mike Fitz
www.3dartz.com