I set my grid in maya to be pixel perfect to my light map res and snapped them to the grid. When I import the new mesh the pixel square meets up at the bottom perfectly, after the bake though it goes back to half a square.
yes the walls have thickness and they did have a blocker around them but I was able to get the white lines to go away after I make a new blocker around the room. The blocker I had before consisted of other rooms and a larger blocker for the whole scene. I guess there was light sneaking in somewhere.