Things like that can happen when you have brushes with sub-unit verticies. This generally happens if you randomly clip peices off of a brush or if you carve brushes with pretty much anything but a square or rectangle.
Check all the vertices on that brush with the grid set to 1 unit, and if anything is off, use vertex manipulation to put the vertices back on the grid.
As for the vis, you probably just have a leak.
Edit: Make sure you haven't accidentally hidden any brushes, too.