Thanks a bunch for your answers!If you've been following the guides right, you've most likely been downloading the Nightlies build for rxTools. They don't tell you which version you have so you MUST know what you downloaded.
Sounds like your NANDs are linked. That's the gift wrap bug that linked users suffer from, only solution is to unlink.
No, the only way is by Nintendo SDK.
Alas, I do not know what I downloaded, there's a package ready to download containing emuNAND and rxTools with no version in its filename... although I got firmware.bin from a friend, because I was on Linux at the time and maybe that batch file that downloads/generaters firmware.bin spits up the version number. Anyway, thanks for your answer.
And my NANDs are definitely unlinked, when I create a folder in emuNAND it does not appear in sysNAND.