First off, Use strict warnings and diagnostics. It'll make debugging a lot easier.

Secondly, try removing the        finddir("$root$file"); from within the foreach loop. You're exiting the loop after the first iteration.

Update: Oops. Read that wrong. Hang on a sec.

Update 2:

my %config = ( home => '/home/cjf/' );
my %user   = ( site_id => 'code'    );

my @alldir = finddir("$config{home}$user{site_id}");
print $_, "\n" for @alldir;

sub finddir {

   my $root = shift;
   chomp $root;
   $root = $root . '/' unless ( $root =~ m|/$| );
   local *DIR;
   opendir DIR, $root or die $!;
   my @userfiles = sort grep !/^\.\.?\z/, readdir DIR;
   my @direct;
   foreach my $file (@userfiles) {
       next unless ( -d "$root$file" );
       my $dir = "$root$file";
       $dir =~ s/^\Q$config{home}$user{site_id}\E//;
       push(@direct, $dir);
   }
   return @direct;
}
[download]

That will return all directories in $config{home}$user{site_id} but not go into the sub directories. Is that what you're looking for?