okay instead of "select matching polys" select "cleanup matching polys" and run cleanup again.
There is clearly a problem with the connection you created and it appears you have some zero area faces or zero length edges.
you may also marquee select the indicated verts and ensure there is only one vert at each of those spots and if not merge them.
if that fails delete all the faces of the connection. Then make sure all the verts at the boundary edges are merged and there is only one vert at each point on the boundary.
Finally, instead of merging point by point do a bridge between the two boundary edges.
"If I have seen further it is by standing on the shoulders of giants." Sir Isaac Newton, 1675
Last edited by ctbram; 03-07-2012 at 10:00 PM.