I've gotten all the plugin settings to work, although I found custom lights a bit more difficult. For example, I put this for a dark dungeon in the map editor note box:
[ambient_light 5]
[ambient_light 000A57]
I also have a switch that turns on/off a common event for day/night cycle, so that day/night doesn't happen in dungeons and such. There are a series of switches and conditionals that change the time of day, so e.g. Night is:
Plugin Command: AmbientLight 10 600
Plugin Command: AmbientLight 000A57 600
That will gradually change the light over 10 seconds. As you can see, the dungeons are darker than the night effect itself, requiring flashlights. The plugin command should also work from an event, so I'd set up a test game with an event where you can select different light levels and experiment. Also take a very close look at Khas's tutorial. I don't think I could have set everything up properly without it.
Does this help at all? If you want the map commands to work, make sure you haven't accidentally turned AutoAmbientLight light off somewhere. I really can't think of anything else. :(