The way I understand it is that you can only disenchant something that was magical before you put an enchant on it. You could have two identical bows, one white, and the green one with a +2 ranged attack on it. You'd get to disenchant the green because of the +2... If you enchanted both of them, you'd still get to enchant the green one because of the previous magical properties, where as the white one is still the same but with an added bonus.
As for green items that aren't disenchanting.. It could be that the item doesn't actually have any magical properties. I think I've seen a few green weapons which were basically just white's with a green name. No special properties.. But I don't know for sure; it's been a long time since I've seen anything like that.