When you do heavy editing extrudes/merging cvs etc, it's a good idea to to dbl-check your verts from time to time...sometimes there will be two though it looks like one...you just have to go through and merge them. As a result of things like this, you can have problems like this if it goes un-detected. At least this is what I've found when it's happened to me. Maybe go back to an earlier save if you have one and check it.