Hm, I'm thinking this is incompatible with 4.1.2. I've got bootloader unlocked, USB debugging enabled, proper drivers installed, everything. When I select an option in the utility and try to run it, I get a message saying "mount:operation not permitted," and my phone boots to the stock recovery screen. Rebooting the phone from there works just fine, so I don't have to re-flash, but this tool refuses to work.
Is your phone rooted? The only reason it would be denying you remount options would be if you have no root access.