I have also been having this problem, it seems to occur when i switch from a craft with a working Lazor System in a different SOI to Kerbin (Minmus) to do other things, i then switch back and the Lazor system is non-functional. Loading an autosave from when it was working doesn't fix it, i can only launch the craft again but that too stops working once i leave it orbiting Minmus and switch away.