Ok, this is very frustrating...
I tried to use your code inside my script like this:

open IN2, $first_tmp;
while(<IN2>)
{
    if($_=~/^(chr.*?)REC:(.*)/)    
    {
        $respective_chrom=$1;
        $all_entries=$2; 

        @split_entries=();
        @split_entries = split(/\#/, $all_entries);    

        @split_sep_entries=();
        %collapsed_loci_HoA=();

        print ">".$respective_chrom."\n";
        foreach $sep_entry(@split_entries)    
        {
            @split_sep_entries = split(/\t/, $sep_entry);
            $locus_to_use = $split_sep_entries[1];
            $rest_entry=$split_sep_entries[0]."\t".$split_sep_entries[
+2]."\t".
                        $split_sep_entries[3]."\t".$split_sep_entries[
+4]."\t".
                        $split_sep_entries[5]."\t".$split_sep_entries[
+6]."\t".
                        $split_sep_entries[7];
            push @{ $collapsed_loci_HoA{$locus_to_use} }, $rest_entry;
        }
        
        $start;
        @answer;

        @array_of_loci = keys %collapsed_loci_HoA;
        
        for (sort { $b <=> $a } @array_of_loci) 
        {
            if( not defined $start or $_ > $start + 1000 )
            {
                push @answer, [ $_ ];
                $start = $_;
            }
            else
            {
            push @{ $answer[-1] }, $_;
            }
        }

        for my $i ( 0 .. $#answer ) 
        {
                 print "$i\t [ @{$answer[$i]} ]\n";
         }
        print "//\n";
    }
}
close IN2;
[download]

and, although, it does create an array with all the elements sorted, it does not create the bins as the standalone snippet does...Any ideas why?