Had the same problem !.I was using the HDInstools on WB 3.1 and was telling me I had minus mb of ram, i tried reading the config and all the other methods, tacks, heads ,cylinders,and still the F++ker would not play ball.
Then I pulled an old Version of HDInstools(V4.2.one that i had with the HD upgrade for my old A500,
and bingo it read the config and recognised the 4+gig barrier no probs !.
Might be of some help.
Good luck