I'm not sure exactly what that program does (never used it) but yeah win32diskimager is the best way to go if on windows, DD if on linux should do the trick nicely, and I think you can get away with that for Mac as well since it's a Unix command.Bad news so. Maybe the jrunner isnt the best choice for make the nand backups.
If that program is for specific NAND readers then I don't think it is going to work for this particular setup since we aren't reading a NAND exactly, it's an eMMC, basically a NAND wrapped up with a controller. This is a pretty simple but good explanation of it from EETimes.
Interesting:
So this JRunner looks like it was built for the Xbox 360 for it's NAND packages.