Since you mention light maps I presume you are baking the light? You said you have already checked your meshes for leaks so its probably lightmass.
In lightmass you generally need to turn the settings up to get a high quality bake that does not penetrate. In your world settings>Lightmass. Try turning your level scale down slightly, your indirect lighting quality up, and your smoothness down. The level scale has the most impact, as it will directly increase your samples. It will have a MAJOR effect on your bake times as well. Try just increasing quality to 3, smoothness to .8, see how it is. If its still bad try taking the scale to .75. In production bakes I have seen scale set to 0.1. Render time jumps to easily 6+ hours for a tiny level.