How do you print them? If there is whitespace at the start or end, they will look similar but still won't run. Also, are you sure that @commands contains regular expressions that will match? Do something like the following:

for my $i (0..$#$commands_run) {
    print "$i: '$commands_run[$i]' =~ /$commands[$i]/";
    print $commands_run[$i] =~ /$commands[$i]/ ? ", Yes" : ", No";
    print "\n";
};
[download]

That should give you a good overview.

Also, you might want to consider instead of having that long if statement using a loop similar to the one I showed for the actual testing. This will also help you to provide better diagnostic output if your test fails, as you can show which condition failed.