The apex of the scene's pettiness has to be this http://wololo.net/2015/03/18/total-noobs-response-to-latest-...
(tl;dr the custom firmware checks if a certain user is using it, if so it formats their memory card)
I don't remember exactly how I fixed it...I think there was some undocumented way to clear the flag that you could only find by reading the tool's source. It was a good reminder of how much stupid, blind trust I tend to put into random tools from the internet.