Works perfectly fine for me. My game save is 2800kb. I'm usually making the changes right onto my USB stick. I used bruteforce to resign my save to a second account where I do all my hybriding with this program. Also I'm on windows xp if that helps.
Could the problems be coming from conflicts with previous edits using other tools or a hex editor? My save was fresh and I've only used this tool since it came out a few hours before I started messing with this.