Okey, Thomas pointed out one thing that is important, the filesystem... if you used an old 3.0/3.1 install disk or something like that to prep or format your harddrive prior to installing 3.9, you're stuck with the old FFS which stops at 4GB... You should make an emergency boot disk with 3.9 and start from scratch again, just to be sure.
Or perhaps just changing the FFS in hdtoolbox and partition the drives above 4GB will do? I dunno... I'll cross my fingers for you!
