Try the attached patch against stable v2.0.6.

I will send another patch shortly against trunk.

Index: cbpolicyd
===================================================================
--- cbpolicyd   (revision 405)
+++ cbpolicyd   (working copy)
@@ -101,7 +101,8 @@
        ) or die "Failed to open config file '".$cfg->{'config_file'}."': $!";
        # Copy config
        my %config = %inifile;
-       untie(%inifile);
+       # FIXME: This now generates a warning as Config::Inifiles doesn't 
implement UNTIE
+       # untie(%inifile);
 
        # Pull in params for the server
        my @server_params = (
@@ -139,13 +140,19 @@
        if (!defined($config{'server'}{'protocols'})) {
                die "Server configuration error: 'protocols' not found";
        }
-       foreach my $module (@{$config{'server'}{'modules'}}) {
-               $module =~ s/\s+//g;
+       # Split off modules
+       my @moduleList = split(/\s+/,$config{'server'}{'modules'});
+       foreach my $module (@moduleList) {
+               # Skip comments
+               next if ($module =~ /^#/);
                $module = "modules/$module";
                push(@{$cfg->{'module_list'}},$module);
        }
-       foreach my $module (@{$config{'server'}{'protocols'}}) {
-               $module =~ s/\s+//g;
+       # Split off protocols
+       my @protocolList = split(/\s+/,$config{'server'}{'protocols'});
+       foreach my $module (@protocolList) {
+               # Skip comments
+               next if ($module =~ /^#/);
                $module = "protocols/$module";
                push(@{$cfg->{'module_list'}},$module);
        }

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