Thank you very much genio!
I didn't realize I had not initialized my $val variable properly. That if statement is no longer nonsense and does the trick. Now header and trailer records are ignored and not processed, thus my count is accurate. I will live with the fact that the unique values it finds are displayed in a 0 based count format, no big deal as it seems to be working like a charm. BTW, did you know that your user name (genio) in spanish means genius? I am guessing you do... lol. Here is the output of a much simpler file:
0:123456789
1:987654321
2:123654874
3:785471236
4:951234569
5:753698741
6:478478478
============
Total Records Processed: 10
Total Unique Values Found : 7

And here is the modified code:

use strict;
use warnings;
use List::MoreUtils qw(uniq);

my $char_at=10;
my $num_chars=50;
my $val;
my @trnAccounts;
#open my $fh, $ARGV[0]
#open my $fh, '<:encoding(UTF-8)', $ARGV[0]
open my $fh, '<:encoding(cp1252)', $ARGV[0]
    or die "Could not open '$ARGV[0]' $!";

while (my $line = <$fh>) {
    $val = substr($line, 0, 1);
    chomp $val;
    if ($val eq 'H' or $val eq 'T') {
        my $output = $line;
    }else {    
        chomp $line;
        next unless $line && length($line) >= $char_at;
        push @trnAccounts, substr($line, $char_at, $num_chars);
    }
}
my @unique_accounts = uniq(@trnAccounts);
print "\n";
for my $i (0..$#unique_accounts) {
    print $i, ":", $unique_accounts[$i], "\n";
}
print "============\n";
print "Total Records Processed: ", scalar(@trnAccounts), "\n";
print "Total Unique Values Found : ", scalar(@unique_accounts), "\n";
[download]

THANK YOU GENIO!