GISD is a different way of doing "GI surface details" from earlier TG2 versions. It's much faster with similar, if not more pleasing, results.
I'm not at liberty to tell how it works.
Crop renders do affect GI, but usually not so much that a crop = complete black shadows, while a full render = brightly lit shadows.
So I would not worry too much about that, but keep in mind that differences *do* occur and that it can vary for each situation.
So I guess it wouldn't hurt if you would increase your crop area and set GI to 4/4/8.
You will notice that the effect of GISD is already greatly reduced with these settings, because you're already sampling GI more accurately now!
So if this doesn't help, then let's think...
How large are those shadow areas, few pixels? Larger areas? TG's GI engine is...well...not the best. Tiny shadows often stay entirely black.
But if your shadows are of reasonable size then there are likely other issues:
1) dark surface shading = dark bounced light = darker shadows
2) GISD is set to values far from the default? If you over-do the AO in conjunction with a large radius then you may introduce very dark shadows.
Turn off GISD or set AO to 0.5 or 0.
How does that work?