You're leaving out a lot of information, for instance what files did you use, where did you place them, what exact method you used to boot the firm, what firmware version you were on, did it even boot into 3DS home menu or did it just power off on its own after CakesFW menu showed up, etc. and most importantly, the exact download you got it from.
There are a lot of user error reasons why this could have happened, but simply booting Cakes, even with firmprot off, wouldn't overwrite firm0/firm1. Otherwise it's possible that something breaks on much older FWs, but you never said what FW you were on despite me asking. 11.4/11.8/11.12 I've personally tested, and there are no issues with.
The only other reason I could think of is if someone made a fake firm specifically designed to restore native firm to firm0/firm1 and passed it off as CakesFW.