How to find unlit points or fence leak points where mobs come from?
Solution 1:
Are all the roofs well lit too? The zombies could be spawning on them and then jump/fall off.
Another options is to install a mod that shows you the locations where mobs can spawn. For example: in Zombe's modpack there is a mod that does just that (all other mods in the pack can be disabled if you want). I've read somewhere that NEI(Not Enough Items) has an option to show the dark spots too.