Any ideas to make capture groups work when patterns defined in INI?

Try

use Config::IniFiles;

my $global_ini_data = Config::IniFiles->new( -file => "test.ini" );
my $regex           = $global_ini_data->val( 'client1', 'rename' );
my $filename        = "201306051200foobar.dat";

eval "sub vodoo { \$_[0] =~ $regex }";
vodoo ( $filename ); # this does in-place edit.

print $filename,$/;
__END__
060520.1200foobar.dat
[download]

If you want a string to be a command, you have to compile it - with string eval. Just the same way as any other perl source is compiled.

update

I admit no having read through all of your code. If you have only one substitution per filename, you could get around with

eval "\$filename =~ $regex";
die $@ if $@;
[download]

Having multiple patterns and clients, you surely don't want to have a named subroutine for each of them. You could construct a dispatch table with

sub makesub {
    # my ($client, $regex) = @_; update: wrong, we have 1 param
    my $regex = shift;
    my $sub = eval "sub { \$_[0] =~ $regex }";
    die $@ if $@;
    return $sub;
}
[download]

and populate a hash with the client identifier as key and the resulting anonymous sub as value, which you then call. Like so:

$hash{$client} = makesub($regex);
$hash{$client}->($filename); # $filename changed
[download]

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