This did the trick.

my @sixad = qq/\/etc\/init.d\/sixad start >tmp2/;
   system( @sixad );
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Here is the updated code. I fixed it up a bit too.

use strict;
use warnings;
use diagnostics;

use Tk;
use Data::Dumper;

require Tk::Pane;
my $mw = MainWindow->new( );

   $| = 1;

   $mw->geometry("300x300");
   $mw->title("TkSixa");
   $mw->protocol( WM_DELETE_WINDOW => \&ask, );

my $SixPairButton = $mw->Button( -text => "START", 
                 -command => \&sixpair, )->pack( -side => "top",
                                 -anchor => "nw", );

my $SixAdButton = $mw->Button( -text => "PAIR", 
                   -command => [ \&sixad, ] )->pack( -side => "top",
                                     -anchor => "nw", );
                                   
my $ClearButton = $mw->Button( -text => "CLEAR", 
                   -command => \&clear, )->pack( -side => "top",
                                 -anchor => "nw", );
                                
my $QuitButton = $mw->Button( -text => "QUIT", 
                  -command => \&stopad, )->pack( -side => "top",
                                 -anchor => "nw", );
                                               
my $Pane = $mw->Scrolled( 'Text', Name => 'Display',
                  -scrollbars => 'e',
              -relief => "sunken",
              -background => "WHITE" )->pack( -side => 'bottom', 
                                -fill => 'both', 
                                -padx => '5', );
              
sub warning {
my $Tlw = $mw->Toplevel;
   $Tlw->title('Warning');

my $Label = $Tlw->Label( -text => 'Please connect controller before pa
+iring.' )->pack( -side => 'top', 
                                                   -pady => '15' );

   $Tlw->Button( -text => "OK",
         -command => sub { $Tlw->withdraw }, )->pack( -side => 'bottom
+', 
                                  -anchor => 'se', 
                                  -padx => '5', 
                                  -pady => '5' );
};

my @file1;
my $OutFile1;
my $Count = 0;
sub sixpair {
   open $OutFile1, "+<", "tmp1", or die "Can't open file: $!";
   @file1 = ();
   
my @sixpair = qw(sixpair >tmp1);
   system( "@sixpair" );  
   
while ( <$OutFile1> ) {
   push(@file1, $_);
   $Pane->insert("end", $_);
   }
   
   $Count = 1;
   return   
   close($OutFile1);
};


sub sixad {
for my $t ( @file1 ) {
   if( $t =~ m/No controller found on USB busses./ ) { 
    &warning; 
    $Count = 0;
    return 
    }
   
   }

if ( $Count gt 0 ) {    

   open my $OutFile2, "+<", "tmp2", or die "Can't open file: $!";
    
my @sixad = qq/\/etc\/init.d\/sixad start >tmp2/;
   system( @sixad );

while( <$OutFile2> ) {
   $Pane->insert("end", $_);
   }

   return;
   close($OutFile2);
   }
      else {
      &warning; 
      return;
      }
      
};

sub ask {
my $Tlw = $mw->Toplevel;
   $Tlw->title('Prompt');

my $Label = $Tlw->Label( -text => 'Are you sure?' )->pack( -side => 't
+op', 
                               -pady => '15' );

   $Tlw->Button( -text => "Quit", 
         -command => \&stopad, )->pack( -side => 'left', 
                             -anchor => 'sw', 
                             -padx => '5', 
                             -pady => '5', );

   $Tlw->Button( -text => "Cancel",
         -command => sub { $Tlw->withdraw }, )->pack( -side => 'right'
+, 
                                  -anchor => 'se', 
                                  -padx => '5', 
                                  -pady => '5' );
};

sub clear { 
$Pane->delete('0.1', 'end');
};

sub stopad {
my @stopad = qw/sixad --stop/;
   system(@stopad);
   exit 0;
};

sub counter {
$Count = '1';
};

MainLoop;


=pod
## If your Bluetooth disappears or stops working run 
hciconfig hci0 up
hciconfig -a

if [[ $(hciconfig -a | grep -o "DOWN") ]]; then 
   echo -e "\nBluetooth is off.\nTurning it on now.\n"; 
   hciconfig set up; 
      else 
      echo -e "\nBluetooth is already on.\n"; 
   fi

=cut
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