I agree with Thomas. Try typing "diskchange dh0:" or hd0: or whatever drive you are trying to format is...
At the very least, it should give you an interesting message, and possibly a hint as to what is wrong.
I would also check to make sure that the drive is set as Master, and that CableSelect is disabled.
I tend to think it's a simple glitch or overlooked setting, and nothing serious.
By the way.... Do yourself a favor. In HDToolBox, go through your partitions, one by one, select it and choose "Change..." Set the MaxTransfer size to "0x1fe00". Do the same thing for each of your partitions. It avoids a wacky buffer glitch in the IDE controller of the A1200/4000. It'll save you the headache of having certain files getting mangled bits tacked on them.