Another thing is when I then go back into HDToolBox it displays the extra partition but when I click on it both that partition and DH3 are selected as if they are one partition and not 2. Strange.
This sounds like a bug in HDToolbox. I have heard that HDtoolbox sometimes creates overlapping partitions, but I never experienced it myself.
How did you start partitioning the HDD ? Did you choose one of the standard setups (1, 2, 4, 8 partitons) and then moved around the partitions HDToolbox created or did you delete all pre-installed partitions and created your own ones one after the other ?
Can you delete all partitions (except the first one if it's already filled with files), save the changes and then check what HDToolbox shows ? Can you delete the dh1_0 partition ?
If you don't get it sorted, please install
tsgui, run it, select one partition of your hdd and choose "save RDB to file" from the menu. Attach the resulting file here or send it to me by e-mail, then I can examine and repair it.
Bye,
Thomas