To me, it sounds like something is going wrong during the rehashing process. I don't see anything about 'saving' on mine. You just take the re-built Xbox EDIT.bin (with the new savegame.txt replacing the old one) and drag/drop it onto the bar in Horizon which says "Drag & drop file here to rehash and resign," wait for it to say it was successful, then drag that same EDIT.bin file from the folder into the USB, as displayed on the right of Horizon. It's weird though, as from what you've said, it seems like you've done everything right. The USB is configured on the Xbox, right? To a minimum of 512mb? Actually it must be, because you said you've got the kits working.
Actually... every time I replace my EDIT.bin file though, I delete the one on the console first, so that the copied one is a clean install. Maybe try that? (Make sure you have the original EDIT.bin backed up first though!) - I seem to remember having a problem with this before, might be that!