I appreciate that this thread is quite old now but I'm still struggling with this issue but I have something to add to the mix - my D600 has behaved as your's did. Luckily I have a docking station powered by the 90w PA10 supply and the batteries all charge on that fine. Given that the software, operating system and hardware are all the same except that the power comes through the docking port instead of the DC jack, I'm assuming that the issue is with the DC input somewhere.
I appreciate that the docking station won't be recognised in the same way by the bios/firmware/os as the ac adaptor plugged into the DC but it does narrow the field a little.
Added to this, I have replaced the DC chasis port on 3 occasions - one was perfect - pain the backside to do but perfect, one was fine except it would not charge the battery and the third, well I never managed to get that one to work at all. This all suggests the DC input to me but nothing definitive.
Did you ever get anywhere with your's?
