Our Phi Sigma Kappa chapter is supported fully by their nationals but now unrecognized by the school because the school is full of jagoffs.
http://www.greekchat.com/gcforums/sh...ad.php?t=76996
A local fraternity, Alpha Gamma Phi, was "underground" for 20 or so years (I think they've finally died out)...the stories as to why they lost their recognition are various.
And finally, TKE at our school operated underground for years (after being kicked off for doing major damage to the Sigma Chi house as well as some Sigma Chis) but for some reason, was recently welcomed back by the school with open arms.