Unless it's been changed, the above shouldn't even work at all; w/ R2012b for two arrays w/o the 'rows' optional argument I get
>> a=randi(4,3,2);b=randi(4,5,2);
>> [c,ia,ib]=intersect(a,b)
Error using intersect>intersectlegacy (line 173)
A and B must be vectors, or 'rows' must be specified.
Error in intersect (line 90)
[varargout{1:nlhs}] = intersectlegacy(varargin{:});
>>
That you "removed the first 2 columns manually" (albeit unspecified which two I presume means the first from each of the two input arrays??) I'd expect it to function correctly.
As is, I've no idea what a current release does; doc doesn't indicate anything different. It indicates that ia, ib are vectors.
