Flan's real problem is not being insane as much as she has no real concept of self control, as I recall. Thus, most people she tries to play with become geography. Fanon has exaggerated her insanity.
Flan isn't so much insane as she's just completely sheltered. Combined with the whole no self control deal and its easy for people to mistaken Flandre as being "bat shit insane".
We must be swift as the coursing river~ With all the force of a great typhoon~ With all the strength of a raging fire~ Mysterious as the dark side of the MOOOOOOOOOON~