First, <code> tags in your posts will help monks interpret your code; see Markup in the Monastery

There are a number of typos in your posted code. As some of these would prevent the interpreter from running, I will assume some of them are from transcription. You do seem to suffer from some misconceptions regarding structures - please read perlref and perldsc. I have attempted to read your mind and fix the posted code - my frobnitz is on the fritz right now, so I can't guarantee this will do what you want.

use strict;
use warnings;
my %LkHigh;
my %leakHigh;
my @names = ('jim', 'john', 'joe');
my @values = (1, 2, 3);
my @PartNums = ('A', 'B', 'C');

# Stage1
for my $i (0 .. $#names) {
    my $name  = $names[$i];
    my $value = $values[$i];
    push @ { $LkHigh{$name}}, $value; # works!
}
#Stage2
for my $PartNum (@PartNums) {
    push @{$leakHigh{$PartNum}}, {%LkHigh};
}
# when I try to print this I loose the $values in the hash array.
# this is what I'm using to print

foreach my $PTnum (keys %leakHigh){
    foreach my $pin (0 .. $#{$leakHigh{$PTnum}}){
        foreach my $i (keys %{$leakHigh{$PTnum}->[$pin]}){
            print "@{$leakHigh{$PTnum}[$pin]{$i}} \n";
        }
    }
}
[download]