There's no need to format the new drive (to NTFS or anything else) as jmfs will handle that. Did you connect the new drive (or the TiVo drive) to your computer and use Windows management to recognize it in the first place? I'm with dwit, I've never heard of anything like what you're experiencing in about a decade of performing upgrades. It could have something to do with your computer's BIOS settings. In any case, keep both drives away from Windows completely (particularly the TiVo drive) it will cause you nothing but grief. As you did, I always disconnect my Windows OS drive when performing an upgrade (unless I'm using winMFS). The jmfs program is dead simple and you shouldn't have any issues. I know that's not helpful, but if you're doing anything at all outside of the instructions/faq you won't get the desired outcome. Best of luck and keep us posted!