Some glowstone blocks will clone without their proper lighting.
I am building a large platform and am using glowstone under 1/2 slabs for lighting and to create a pattern only seen at night. I am cloning about 20,600 block segments of the platform. As I clone some of the clones segment will often be unlit and requires me to place a block and remove it to activate most of the glowstone. However after doing this there are many glowstones that will be blacked out and others will suffer a brownout where they are at about 1/2 of their normal illumination. I must go through the clones segment and re activate the glowstone by placing a glowstone in the affected area and removing it to cause a block update.
I am attaching pictures of the cloned platform after I activate the bulk of the segment and some exposed glowstone in its blackout state.
I am currently using the city texture pack but have this issue with the standard texture pack as well.