First: always use strictures (use strict; use warnings;). $cmd and each of the variables assigned to within the first loop should be declared with my to make it clear that they are local to the loop.

Your 'hash concatenation' trick is horrible! For a better technique have a look at the code below.

As far as I can tell it works for me using some invented data:

use strict;
use warnings;

my %cmdData = map {$_ => {opcode => 1, cmd => 2}} ('a' .. 'b');
my %fssaCmd = map {$_ => {fixed_pattern => 1}} (1 .. 6);
my $ApidBase = 0;
my $ApidOffset = 0;

foreach my $cmd (keys %fssaCmd) {
    my $opcode = sprintf("%x", $fssaCmd{$cmd}{fixed_pattern});
    my $apid   = sprintf("%x", $ApidBase + $ApidOffset);
    print("$cmd, 0x$apid, 0x$opcode\n");
    $cmdData{"0x$apid"} = {opcode => "0x$opcode", cmd => $cmd};
}

foreach my $a (sort keys %cmdData) {
    print $a. ", " . $cmdData{$a}{opcode} . ", " . $cmdData{$a}{cmd} .
+ "\n";
}
[download]

Prints:

6, 0x0, 0x1
4, 0x0, 0x1
1, 0x0, 0x1
3, 0x0, 0x1
2, 0x0, 0x1
5, 0x0, 0x1
0x0, 0x1, 5
a, 1, 2
b, 1, 2
[download]

Maybe you need to show us a sample of 'real' data that is causing trouble?