Sometimes you can fix those lighting glitches by right-clicking somewhere within the glitched area with basically anything; empty hands or items without right-click actions are recommended because they won't break anything.
If that doesn't work, place (and then break) torches in or next to the dark spots. That'll trigger lighting updates for sure.
Alternatively, MCEdit has a feature where it'll automatically fix any and all lighting glitches whenever you save a world opened in it; however, it assumes all mod blocks to be opaque so all your mod glass, cables, and such will be dark; but everything else will be fine.