I've fixed some issues with r1 and added a little bit of debug output for close vertexes. If you see something like:
Min vertex diff 0.0555317 at (328, 988, 56).
You might want to check that area out. Sometimes it's due to weird splits with qbsp, but a lot of the time, it's due to brushes that are very slightly misaligned, which will result in potentially visible gaps in the polygons.