Okay, tracked it down. So on rarefaction, it is possible to have vectors that get dropped out (eg, sum(vec) < n), and additionally, possible to have vectors on the opposite axis get zerod depending on the rarefaction. I think this is what you were eluding to with the restriction -- the way I'm doing the rarefaction in cython is such that it is zeroing out vectors directly when sum(vec) < n, and that may be partially driving this. 

It'd be awesome if we could do this without incurring both filters, will continue to look and toy