bug in linkage function

If you load the links variable defined in this mat file (12MB):

www.cs.cmu.edu/~cdoersch/links.mat

and then run the following code in Matlab R2012a:

 cluststr=linkage((1:25000)','average',{@(x,y) -links(x,y)+13});

linkage is not mine; it's part of the stats toolbox. You get this error:

 In an assignment  A(I) = B, the number of elements in B and I must be the same.
    file: '/code/MATLAB/R2012b/toolbox/stats/stats/linkage.m'
    name: 'fixnonchronologicalZ'
    line: 443

    file: '/code/MATLAB/R2012b/toolbox/stats/stats/linkage.m'
    name: 'rearrange'
    line: 422

    file: '/code/MATLAB/R2012b/toolbox/stats/stats/linkage.m'
    name: 'linkage'
    line: 256

Sorry about the weird formatting--running this from within a framework, but I doubt that's the issue.

Anyway, fixnonchronologicalZ seems to be trying to relabel the nodes to make them look tidy. However, the algorithm for doing so seems to assume that each node occurs at least once in columns one and two of Z. This is almost true, but not for the root node. My case seems to require that the algorithm relabel the root node. Here's my fix:

 function Z = fixnonchronologicalZ(Z)
 % Fixes a binary tree that has branches defined in a non-chronological order  

 nl = size(Z,1)+1; % number of leaves
 nb = size(Z,1); % number of branches
 last = nl; % last defined node, we start only with leaves
 for i = 1:nb
    tn = nl+i; %this node
    if any(Z(i,[1,2])>last)
        % this node (tn) uses nodes not defined yet, find a node (h) that
        % does use nodes already defined so we can interchange them:
        h = find(all(Z(i+1:end,[1 2])<=last,2),1)+i;
        % change nodes:
        Z([i h],:) = Z([h i],:);
        nn = nl+h; % new node
        % change references to such nodes
 --     Z([find(Z(1:2*nb) == nn,1) find(Z(1:2*nb) == tn,1)]) = [tn nn];          
 ++     tonn=find(Z(1:2*nb) == tn,1);
 ++     Z([find(Z(1:2*nb) == nn,1)]) = [tn];
 ++     if(~isempty(tonn))
 ++       Z(tonn) = [nn];
 ++     end
    end
    last = tn;
 end

I think this fixes the problem, but I'm not entirely sure it's correct since I'm not 100% sure what fixnonchronologicalZ is supposed to be doing. Can somebody check my code and make sure?