I've had this problem before. It can get to the point where the only way is to move/add your lighting in the grid view either top, front or side. then recompile. It can become a pain in the ass as you will need to do this over and over as you add/move lights so you'll be doing a lot of recompiles.

or sometimes if you highlight all of your lighting and delete it all then recompile your map and start the lighting over the problem will go away.