Hah, welcome to the quirkiness of the 3DS. Some things are just unexplainable. Like how only europeans have problems with reinand in general.
Anyways, if CN launches it, then yea, its not the CFW or location of it.. CN is just a means of gaining arm9 and i basically use a brahma like setup to read reinand.dat into ram and execute at 0x12000 or w/e i currently have the entrypoint set to. MSET on the other hand, uses the dsprofile to gain arm9 by writing the rop loader to the dsprofile via flash card. I assume this is the rop FBI uses, precisely (More specifically, the dsprofile rop manipulates system settings API to read rop from reinand.dat, and that rop is what gains arm9).
That aside, if CN works, its not the CFW itself, and if MSET works for some its not FBI thats a problem. Have you tried using the rop installer i have on git? Does the FBI rop just crash back to homemenu with that white popup box?