I bet that @commands does not contain regex patterns, but you treat its contents as such.

=~ /$commands[0]/         # Matches pattern in $commands[0]
=~ /\Q$commands[0]\E/     # Contains string in $commands[0]
=~ /^\Q$commands[0]\E\z/  # Equals string in $commands[0]
eq $commands[0]           # Equals string in $commands[0]
[download]

\Q..\E is a shortcut for calling quotemeta.

And here's a solution that avoids redundancy:

if (
    grep { $commands_run[$_] ne $commands[$_] } 0..$#commands
) {
    print "Test ---- FAIL\n";
} else {
    print "Test -----PASS\n";
}
[download]