Here's your problem:
Installing /usr/wombat/lib/RT/Queue_SLA.pm
<...>
pkg_info: /usr/wombat/share/rt38/plugins/RT-Extension-SLA/lib/RT/Queue_SLA.pm 
doesn't exist

The port actually installs in ${PREFIX}/lib while pkg-plist expects files in ${PREFIX}/rt38/plugins.

It's quite the same problem as with www/p5-RTx-Statistics (http://lists.freebsd.org/pipermail/freebsd-perl/2009-July/002242.html).

An ugly assumption that environment variable PREFIX actually points to ${PREFIX}/rt38. I think letting Perl figure out where RT actually is is a better idea.

--
Cezary Morga
"The world is a tragedy to those who feel, but a comedy to those who think." (Horace Walpole)
--- inc/Module/Install/RTx.pm.orig      2009-04-24 21:01:47.000000000 +0000
+++ inc/Module/Install/RTx.pm   2009-07-13 20:18:23.696711396 +0000
@@ -34,13 +34,10 @@ sub RTx {
         unless $self->abstract;
 
     my @prefixes = (qw(/opt /usr/local /home /usr /sw ));
-    my $prefix   = $ENV{PREFIX};
+    my $prefix   = $ENV{LOCALBASE};
+    push @prefixes, $prefix;
     @ARGV = grep { /PREFIX=(.*)/ ? ( ( $prefix = $1 ), 0 ) : 1 } @ARGV;
 
-    if ($prefix) {
-        $RT::LocalPath = $prefix;
-        $INC{'RT.pm'} = "$RT::LocalPath/lib/RT.pm";
-    } else {
         local @INC = (
             @INC,
             $ENV{RTHOME} ? ( $ENV{RTHOME}, "$ENV{RTHOME}/lib" ) : (),
@@ -53,7 +50,6 @@ sub RTx {
             $_ = $self->prompt("Path to your RT.pm:") or exit;
             push @INC, $_, "$_/rt3/lib", "$_/lib/rt3", "$_/lib";
         }
-    }
 
     my $lib_path = File::Basename::dirname( $INC{'RT.pm'} );
     my $local_lib_path = "$RT::LocalPath/lib";
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