Alright this is from memory, and I'm old, so...
let's see, I put dlditool, g6fl.dldi, and dsorganize.nds in the same directory on my windows desktop.
I didn't write a batch file.. I just used the RUN option in the Start menu and browsed to the directory, then clicked dlditool and added the "g6fl.dldi dsorganize.nds" to the end of the text field. It ran quickly and invisibly, but changed the "modified" date on the .nds file.
From there I just dragged dsorganize.nds into the G6 card at the root level, ejected, slapped it in my DS and went to My Card in the G6 Lite menu, touched the dsorganize.nds file and selected "add header"... and it ran, and saved, and all that good stuff.
By the way, if you haven't updated your card to the 4.6C firmware... do it now, that might be your problem!?!