Ok, Here is the fix.

First of all in nph_build you need to replace this

print "This phase of step 2 took $elapsed seconds.\n\n";
($offset > $#categories) ?

with this

print "This phase of step 2 took $elapsed seconds.\n\n";
($offset > $#category_list) ?

this was wrong in the origional code and stopped staggered from working. Auto worked although.

Now the problem is build_stats is not run before categories are build so you need to replace

($step == 2) and do {
my @category_list = &category_list;
my $i;
print $header;
if ($auto) {

with this
($step == 2) and do {
my @category_list = &category_list;
my $i;
print $header;

print "Build Stats .. \n";
$t1 = time();
print "** Loading Summary information . . .\n";
&build_stats (1);
if ($auto) {

Now rebuild and it shows all links with alt cats in those cats.